sbuild (Debian sbuild) 0.79.1 (22 April 2020) on carme.larted.org.uk +==============================================================================+ | seqan2 2.4.0+dfsg-12 (amd64) Mon, 05 Oct 2020 18:37:00 +0000 | +==============================================================================+ Package: seqan2 Version: 2.4.0+dfsg-12 Source Version: 2.4.0+dfsg-12 Distribution: sid Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-debomatic-8998ae94-c10f-471c-988c-d52cc337937a' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup seqan2_2.4.0+dfsg-12 sid amd64 ----------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup seqan2_2.4.0+dfsg-12 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/seqan2-3ykAU4/resolver-XCnnyL' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [146 kB] Get:2 http://localhost:3142/debian sid InRelease [146 kB] Get:3 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-05-0800.58.pdiff [4170 B] Get:5 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-05-1407.40.pdiff [14.6 kB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-05-1407.40.pdiff [14.6 kB] Get:6 http://localhost:3142/debian sid/main Sources.diff/Index [27.9 kB] Get:7 http://localhost:3142/debian sid/main Sources 2020-10-05-0800.58.pdiff [7387 B] Get:8 http://localhost:3142/debian sid/main Sources 2020-10-05-1407.40.pdiff [15.5 kB] Get:8 http://localhost:3142/debian sid/main Sources 2020-10-05-1407.40.pdiff [15.5 kB] Fetched 390 kB in 2s (242 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/seqan2_2.4.0+dfsg-12.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/seqan2-3ykAU4/seqan2-2.4.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/seqan2-3ykAU4' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), python3, cmake, fakeroot, build-essential, fakeroot, zlib1g-dev, libbz2-dev, libbam-dev, libboost-dev, help2man, ctdconverter Filtered Build-Depends: debhelper-compat (= 12), python3, cmake, fakeroot, build-essential, fakeroot, zlib1g-dev, libbz2-dev, libbam-dev, libboost-dev, help2man, ctdconverter dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [426 B] Get:5 copy:/<>/apt_archive ./ Packages [501 B] Fetched 1884 B in 0s (99.1 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils build-essential cmake cmake-data ctdconverter debhelper dh-autoreconf dh-strip-nondeterminism dpkg-dev dwz fakeroot file g++ g++-10 gcc gcc-10 gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13 libasan6 libbam-dev libboost-dev libboost1.71-dev libbrotli1 libbz2-dev libc6-dev libcroco3 libcrypt-dev libcurl4 libdebhelper-perl libdpkg-perl libelf1 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgcc-10-dev libglib2.0-0 libgssapi-krb5-2 libicu67 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libperl5.30 libpipeline1 libprocps8 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libssl1.1 libstdc++-10-dev libsub-override-perl libtool libubsan1 libuchardet0 libuv1 libxml2 libxslt1.1 m4 man-db mime-support perl perl-modules-5.30 po-debconf procps python3 python3-ctdopts python3-lxml python3-minimal python3-pkg-resources python3-ruamel.yaml python3-ruamel.yaml.clib python3-tz python3.8 python3.8-minimal sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build cwl-runner dh-make debian-keyring g++-multilib g++-10-multilib gcc-10-doc gcc-multilib manpages-dev flex bison gdb gcc-doc gcc-10-multilib gcc-10-locales gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.71-doc libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-filesystem1.71-dev libboost-graph1.71-dev libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-program-options1.71-dev libboost-python1.71-dev libboost-random1.71-dev libboost-regex1.71-dev libboost-serialization1.71-dev libboost-stacktrace1.71-dev libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-dev glibc-doc git bzr krb5-doc krb5-user libstdc++-10-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl libtap-harness-archive-perl libmail-box-perl python3-doc python3-tk python3-venv python3-lxml-dbg python-lxml-doc python3-setuptools python3.8-venv python3.8-doc binfmt-support Recommended packages: libalgorithm-merge-perl curl | wget | lynx bzip2-doc ca-certificates libfile-fcntllock-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl psmisc python3-bs4 python3-html5lib The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils build-essential cmake cmake-data ctdconverter debhelper dh-autoreconf dh-strip-nondeterminism dpkg-dev dwz fakeroot file g++ g++-10 gcc gcc-10 gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libarchive13 libasan6 libbam-dev libboost-dev libboost1.71-dev libbrotli1 libbz2-dev libc6-dev libcroco3 libcrypt-dev libcurl4 libdebhelper-perl libdpkg-perl libelf1 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgcc-10-dev libglib2.0-0 libgssapi-krb5-2 libicu67 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libperl5.30 libpipeline1 libprocps8 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libssl1.1 libstdc++-10-dev libsub-override-perl libtool libubsan1 libuchardet0 libuv1 libxml2 libxslt1.1 m4 man-db mime-support perl perl-modules-5.30 po-debconf procps python3 python3-ctdopts python3-lxml python3-minimal python3-pkg-resources python3-ruamel.yaml python3-ruamel.yaml.clib python3-tz python3.8 python3.8-minimal sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 97 newly installed, 0 to remove and 0 not upgraded. Need to get 90.1 MB of archives. After this operation, 472 MB of additional disk space will be used. 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amd64 libprocps8 amd64 2:3.3.16-5 [62.7 kB] Get:23 http://localhost:3142/debian unstable/main amd64 procps amd64 2:3.3.16-5 [262 kB] Get:24 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:27 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:28 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:30 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:31 http://localhost:3142/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:32 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:33 http://localhost:3142/debian 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http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:88 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:89 http://localhost:3142/debian unstable/main amd64 debhelper all 13.2.1 [1007 kB] Get:90 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.25.2-1 [46.9 kB] Get:91 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.25.2-1 [86.8 kB] Get:92 http://localhost:3142/debian unstable/main amd64 help2man amd64 1.47.16 [181 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libbam-dev amd64 0.1.19-4 [125 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libboost1.71-dev amd64 1.71.0-6+b2 [9097 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libboost-dev amd64 1.71.0.3 [4340 B] Get:96 http://localhost:3142/debian unstable/main amd64 libbz2-dev amd64 1.0.8-4 [30.1 kB] Get:97 http://localhost:3142/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 90.1 MB in 1s (162 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 10509 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36-3+b1_amd64.deb ... Unpacking bsdextrautils (2.36-3+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.3-2_amd64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package perl-modules-5.30. Preparing to unpack .../05-perl-modules-5.30_5.30.3-4_all.deb ... Unpacking perl-modules-5.30 (5.30.3-4) ... 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Setting up autoconf (2.69-11.1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up procps (2:3.3.16-5) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libxslt1.1:amd64 (1.1.34-4) ... Setting up libcurl4:amd64 (7.72.0-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up python3-pkg-resources (49.3.1-2) ... Setting up automake (1:1.16.2-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up libstdc++-10-dev:amd64 (10.2.0-13) ... Setting up g++-10 (10.2.0-13) ... Setting up libtool (2.4.6-14) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up python3-ctdopts (1.4-1) ... Setting up libdebhelper-perl (13.2.1) ... Setting up libboost1.71-dev:amd64 (1.71.0-6+b2) ... Setting up python3-ruamel.yaml.clib (0.2.0-3) ... Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gcc (4:10.2.0-1) ... Setting up dpkg-dev (1.20.5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.47.16) ... Setting up python3-ruamel.yaml (0.16.10-2) ... Setting up g++ (4:10.2.0-1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up python3-lxml:amd64 (4.5.2-1) ... Setting up cmake (3.18.2-1) ... Setting up build-essential (12.8) ... Setting up libboost-dev:amd64 (1.71.0.3) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up po-debconf (1.0.21) ... Setting up ctdconverter (2.1-3) ... /usr/lib/python3/dist-packages/galaxy/converter.py:397: SyntaxWarning: "is" with a literal. Did you mean "=="? elif TYPE_TO_GALAXY_TYPE[param.type] is 'text': Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up debhelper (13.2.1) ... Setting up dh-autoreconf (19) ... 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Processing triggers for libc-bin (2.31-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.7.0-2-amd64 #1 SMP Debian 5.7.10-1 (2020-07-26) amd64 (x86_64) Toolchain package versions: binutils_2.35.1-1 dpkg-dev_1.20.5 g++-10_10.2.0-13 gcc-10_10.2.0-13 libc6-dev_2.31-3 libstdc++-10-dev_10.2.0-13 libstdc++6_10.2.0-13 linux-libc-dev_5.8.10-1 Package versions: adduser_3.118 apt_2.1.10 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-7 binutils_2.35.1-1 binutils-common_2.35.1-1 binutils-x86-64-linux-gnu_2.35.1-1 bsdextrautils_2.36-3+b1 bsdutils_1:2.36-3+b1 build-essential_12.8 bzip2_1.0.8-4 cmake_3.18.2-1 cmake-data_3.18.2-1 coreutils_8.32-4+b1 cpp_4:10.2.0-1 cpp-10_10.2.0-13 cpp-7_7.5.0-6 ctdconverter_2.1-3 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debian-archive-keyring_2019.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5 dpkg-dev_1.20.5 dwz_0.13-5 e2fsprogs_1.45.6-1 eatmydata_105-9 fakeroot_1.25.2-1 fdisk_2.36-3+b1 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.2.0-1 g++-10_10.2.0-13 gcc_4:10.2.0-1 gcc-10_10.2.0-13 gcc-10-base_10.2.0-13 gcc-7-base_7.5.0-6 gcc-8-base_8.4.0-4 gcc-9-base_9.3.0-18 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 help2man_1.47.16 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan4_7.5.0-6 libasan6_10.2.0-13 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbam-dev_0.1.19-4 libbinutils_2.35.1-1 libblkid1_2.36-3+b1 libboost-dev_1.71.0.3 libboost1.71-dev_1.71.0-6+b2 libbrotli1_1.0.9-2 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-3 libc-dev-bin_2.31-3 libc6_2.31-3 libc6-dev_2.31-3 libcap-ng0_0.7.9-2.2 libcc1-0_10.2.0-13 libcilkrts5_7.5.0-6 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-1 libctf0_2.35.1-1 libcurl4_7.72.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5 libeatmydata1_105-9 libelf1_0.181-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.2-1 libfdisk1_2.36-3+b1 libffi6_3.2.1-9 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-13 libgcc-s1_10.2.0-13 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm5_1.14.1-6+b1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.0-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-13 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libhogweed4_3.5.1+really3.4.1-1 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10.2.0-13 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libksba8_1.4.0-2 libldap-2.4-2_2.4.53+dfsg-1 libldap-common_2.4.53+dfsg-1 liblocale-gettext-perl_1.07-4 liblsan0_10.2.0-13 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3+b1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libmpx2_8.4.0-4 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle6_3.5.1+really3.4.1-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 libnpth0_1.6-2 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.26_5.26.2-7+b1 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libprocps8_2:3.3.16-5 libpsl5_0.21.0-1.1 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.6-1 libpython3.8-stdlib_3.8.6-1 libquadmath0_10.2.0-13 libreadline7_7.0-5 libreadline8_8.0-4 librhash0_1.4.0-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.4-1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2 libsmartcols1_2.36-3+b1 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-13 libstdc++6_10.2.0-13 libsub-override-perl_0.09-2 libsystemd0_246.6-1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtool_2.4.6-14 libtsan0_10.2.0-13 libubsan0_7.5.0-6 libubsan1_10.2.0-13 libuchardet0_0.0.7-1 libudev1_246.6-1 libunistring2_0.9.10-4 libuuid1_2.36-3+b1 libuv1_1.39.0-1 libxml2_2.9.10+dfsg-6 libxslt1.1_1.1.34-4 libzstd1_1.4.5+dfsg-4 linux-libc-dev_5.8.10-1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.36-3+b1 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.26_5.26.2-7 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 procps_2:3.3.16-5 python3_3.8.2-3 python3-ctdopts_1.4-1 python3-lxml_4.5.2-1 python3-minimal_3.8.2-3 python3-pkg-resources_49.3.1-2 python3-ruamel.yaml_0.16.10-2 python3-ruamel.yaml.clib_0.2.0-3 python3-tz_2020.1-2 python3.8_3.8.6-1 python3.8-minimal_3.8.6-1 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-3+b1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: seqan2 Binary: seqan-apps, libseqan2-dev Architecture: any all Version: 2.4.0+dfsg-12 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe , Kevin Murray Homepage: http://www.seqan.de/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/seqan2 Vcs-Git: https://salsa.debian.org/med-team/seqan2.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, libbam-dev, libboost-dev, libbz2-dev, zlib1g-dev Build-Depends: debhelper-compat (= 12), python3, cmake, fakeroot Build-Depends-Arch: zlib1g-dev, libbz2-dev, libbam-dev, libboost-dev, help2man, ctdconverter Package-List: libseqan2-dev deb libdevel optional arch=all seqan-apps deb science optional arch=any Checksums-Sha1: 119b812a854d626deb890762ef57e6a1b2ced0ff 84125556 seqan2_2.4.0+dfsg.orig.tar.xz 17b16f3af3f4ce4a11f30e07ea8cb2c9ef77b37e 28848 seqan2_2.4.0+dfsg-12.debian.tar.xz Checksums-Sha256: 9e69ff4130519b9c9bf019df6faaa280f35d9fd0485cfcfe270c525744bbe86e 84125556 seqan2_2.4.0+dfsg.orig.tar.xz b9936b86aa961c1c9a4a5f977660c47f9b4f0bbff60e9f354bef735ee2d4042f 28848 seqan2_2.4.0+dfsg-12.debian.tar.xz Files: c0a126276b1b2864cde3a3b00a7516b5 84125556 seqan2_2.4.0+dfsg.orig.tar.xz 74e69cf6f0e57b2c158d733e2df50f65 28848 seqan2_2.4.0+dfsg-12.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl4+9LAACgkQPCZ2P2xn 5uIW4w//WwIDrI4x9HwDo7KKlO4QjBBA0U2OG6zaUDLw5XUHK0aljBodU3uIt7AG LGONIZl8cTCopI9utou6L9a5kU1i8tPrGUWD43L7bp8BVd5GAkUlKWmVbcZmDbRr nc/0nNzib6o0BC0uEHqYuUCs+Jp7mxykAfuap6cnHjGuzMbhE03Pm78t1g+y/dKF Y4sKnBBuOLNk4tdaKOHYosBAaCb+lubLf/FfcA8RafT+kVrJjoyk0wtrHITsB6UX 58aeWYFRKDdP8INvez7jweN7F0ZQamtKJPNDNFaZBFQEsqduYLZ0AShHljMbYYrl IqyJnfwfdiKswrPsxyT0B0cSiW0CTkEpVF0DWCZOuvsGPEGExo+h78ls/Sjzi7Ll stbUw3bLMddBczGxeeLkX5plTJKSSY7CEFt885lXqYVMVD6igpKBYLmNIX575lWx syfmDZB4vt96qi72VHoBRv17lE5HCmUMtaenDPRsRBCYfPulH9RGvQi8BQbTRyQ3 hz6Ximeyfze0QCX83Nb2LxFyT5/HPKDUVquRvnYH8NC/xe1NmVTvkZriSf9nJ2Ny kIwX1lfnOx5f1aZSOQx5fEyCOdw5ffEicbBKsmH7RUpYRHQFAkLBaMmGFopP6xLr g6b7B3U7EC1OWXbP+X8nNg/UetchHOoDraXMaPKrstYa6r5IpRw= =WwFE -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.govoUK1E/trustedkeys.kbx': General error gpgv: Signature made Sat Feb 8 17:49:36 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./seqan2_2.4.0+dfsg-12.dsc dpkg-source: info: extracting seqan2 in /<> dpkg-source: info: unpacking seqan2_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking seqan2_2.4.0+dfsg-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying skip-seqan-revision dpkg-source: info: applying fix-version_check-test dpkg-source: info: applying skip-some-apps-on-some-archs dpkg-source: info: applying tweak_readmes dpkg-source: info: applying install_fiona_illumina dpkg-source: info: applying ctdVersion.patch dpkg-source: info: applying fix_manpage_formatting.patch dpkg-source: info: applying no-unaligned-access.patch dpkg-source: info: applying ia64_yield dpkg-source: info: applying python3 Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network seqan2_2.4.0+dfsg-12 sid amd64 ----------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network seqan2_2.4.0+dfsg-12 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1001/bus HOME=/sbuild-nonexistent LANG=C LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=sid-amd64-debomatic SCHROOT_CHROOT_NAME=sid-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=112 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=sid-amd64-debomatic-8998ae94-c10f-471c-988c-d52cc337937a SCHROOT_UID=1001 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic XDG_RUNTIME_DIR=/run/user/1001 XDG_SESSION_CLASS=background XDG_SESSION_ID=c4013947 XDG_SESSION_TYPE=unspecified dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package seqan2 dpkg-buildpackage: info: source version 2.4.0+dfsg-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean find . -type f -name "*.pyc" -delete if [ -d orig ] ; then \ for header in `find orig -name "*generated_forwards.h"` ; do \ mv ${header} `echo $header | sed 's?orig/??'` ; \ done ; \ fi rm -rf orig make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/seqan-apps.substvars debian/libseqan2-dev.substvars debian/files rm -fr -- debian/seqan-apps/ debian/tmp/ debian/libseqan2-dev/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building seqan2 using existing ./seqan2_2.4.0+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building seqan2 in seqan2_2.4.0+dfsg-12.debian.tar.xz dpkg-source: info: building seqan2 in seqan2_2.4.0+dfsg-12.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/<>' export DEB_BUILD_ARCH=amd64 ; \ dh_auto_configure --arch -- \ -DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 \ -DSEQAN_DISABLE_VERSION_CHECK=YES install -d obj-x86_64-linux-gnu cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 -DSEQAN_DISABLE_VERSION_CHECK=YES .. -- The CXX compiler identification is GNU 10.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Initializing SeqAn Build System... -- Scanning dependencies once in DEVELOP mode... -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.71.0/BoostConfig.cmake (found version "1.71.0") -- Performing Test CXX14_BUILTIN -- Performing Test CXX14_BUILTIN - Success -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found Seqan: /<>/include (found version "2.4.0") -- Selected repository dir: /<> -- Repository date not determined. -- Repository revision not determined. -- Configuring tests -- Configuring tests -- Configuring tests/align -- Could NOT find SDE: Intel(R) Software Development Emulator (sde) (missing: SDE_EXECUTABLE SDE_VERSION_STRING) -- Could NOT find Umesimd (missing: UMESIMD_INCLUDE_DIR) -- Performing Test SSE4_SOURCE_RUNS -- Performing Test SSE4_SOURCE_RUNS - Success (Compiled & Host CPU support) -- Performing Test AVX2_SOURCE_RUNS -- Performing Test AVX2_SOURCE_RUNS - Success (Compiled & Host CPU support) -- Performing Test AVX512_KNL_SOURCE_RUNS -- Performing Test AVX512_KNL_SOURCE_RUNS - Failed -- => Abort simd detection of newer instruction sets -- Performing Test SEQAN_SIMD_SEQANSIMD_SUPPORTED -- Performing Test SEQAN_SIMD_SEQANSIMD_SUPPORTED - Success -- Performing Test SEQANSIMD_AVX512_KNL_SOURCE_RUNS -- Performing Test SEQANSIMD_AVX512_KNL_SOURCE_RUNS - Success (Compiled) -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. -- Configuring tests/align_extend -- Configuring tests/align_parallel -- Could NOT find SDE: Intel(R) Software Development Emulator (sde) (missing: SDE_EXECUTABLE SDE_VERSION_STRING) -- Could NOT find Umesimd (missing: UMESIMD_INCLUDE_DIR) -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. -- Configuring tests/align_profile -- Configuring tests/align_split -- Configuring tests/alignment_free -- Configuring tests/arg_parse -- Configuring tests/bam_io -- Configuring tests/basic -- Configuring tests/bed_io -- Configuring tests/blast -- Configuring tests/consensus -- Configuring tests/consensus_v2 -- Configuring tests/find -- Configuring tests/gff_io -- Configuring tests/graph_algorithms -- Configuring tests/graph_align -- Configuring tests/graph_msa -- Configuring tests/graph_types -- Configuring tests/index -- Configuring tests/journaled_set -- Configuring tests/journaled_string_tree -- Configuring tests/map -- Configuring tests/misc -- Configuring tests/modifier -- Configuring tests/modifier_cyclic_shape -- Configuring tests/multiple_translation_units -- Configuring tests/parallel -- Configuring tests/parse_lm -- Configuring tests/pipe -- Configuring tests/platform -- Configuring tests/random -- Configuring tests/realign -- Configuring tests/reduced_aminoacid -- Configuring tests/rna_io -- Configuring tests/roi_io -- Configuring tests/score -- Configuring tests/seeds -- Configuring tests/seq_io -- Configuring tests/sequence -- Configuring tests/sequence_journaled -- Configuring tests/simd -- Could NOT find SDE: Intel(R) Software Development Emulator (sde) (missing: SDE_EXECUTABLE SDE_VERSION_STRING) -- Could NOT find Umesimd (missing: UMESIMD_INCLUDE_DIR) -- Intel Software Development Emulator not found, not building platform emulated tests. -- Configuring tests/simple_intervals_io -- Configuring tests/statistics -- Configuring tests/store -- Configuring tests/stream -- Configuring tests/find_swift -- Configuring tests/tabix_io -- Configuring tests/translation -- Configuring tests/test_ucsc_io -- Configuring tests/vcf_io -- Configuring demos -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps -- Configuring apps/alf -- Configuring apps/bs_tools -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/dfi -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/fiona -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/fx_tools -- Configuring apps/gustaf -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/insegt -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/mason2 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/micro_razers -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/ngs_roi -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/pair_align -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/param_chooser -- Configuring apps/rabema -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/razers -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/razers3 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/rep_sep -- Configuring apps/sak -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/sam2matrix -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/samcat -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/searchjoin -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/seqan_tcoffee -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/seqcons2 -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/sgip -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/snp_store -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/splazers -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/stellar -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/tree_recon -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/yara -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /<>/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>' rm -f debian/seqan-apps.debhelper.log debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/<>' dh_auto_configure --indep -B build -- \ -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY -DSEQAN_NO_DOX=1 install -d build cd build && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY -DSEQAN_NO_DOX=1 .. -- The CXX compiler identification is GNU 10.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Initializing SeqAn Build System... -- Selected repository dir: /<> -- Repository date not determined. -- Repository revision not determined. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /<>/build make[1]: Leaving directory '/<>' rm -f debian/libseqan2-dev.debhelper.log debian/rules override_dh_auto_build-arch make[1]: Entering directory '/<>' dh_auto_build --arch --max-parallel=2 cd obj-x86_64-linux-gnu && make -j2 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/CMakeFiles/seqan_library.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/mason2 /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/mason2 /<>/obj-x86_64-linux-gnu/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake --color= Scanning dependencies of target seqan_library make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/seqan_library.dir/build'. make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 0%] Built target seqan_library make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/DependInfo.cmake --color= Scanning dependencies of target mason_sim make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build Scanning dependencies of target pair_align_global_1001 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -c /<>/apps/mason2/external_split_merge.cpp [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/mason2/external_split_merge.h:52, from /<>/apps/mason2/external_split_merge.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/external_split_merge.h:52, from /<>/apps/mason2/external_split_merge.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/external_split_merge.h:52, from /<>/apps/mason2/external_split_merge.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/mason2/external_split_merge.h:52, from /<>/apps/mason2/external_split_merge.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/external_split_merge.h:52, from /<>/apps/mason2/external_split_merge.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/external_split_merge.h:52, from /<>/apps/mason2/external_split_merge.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/external_split_merge.h:52, from /<>/apps/mason2/external_split_merge.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/external_split_merge.h:52, from /<>/apps/mason2/external_split_merge.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -c /<>/apps/mason2/genomic_variants.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/genomic_variants.h:52, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = GenomicInterval]’: /<>/include/seqan/misc/interval_tree.h:1502:18: required from ‘void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2) [with TValue = int; TCargo = GenomicInterval; TValue2 = int]’ /<>/apps/mason2/genomic_variants.cpp:718:51: required from here /<>/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/mason2/genomic_variants.h:49, from /<>/apps/mason2/genomic_variants.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/mason_options.cpp.o -c /<>/apps/mason2/mason_options.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/mason2/mason_options.h:51, from /<>/apps/mason2/mason_options.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/mason2/mason_options.h:51, from /<>/apps/mason2/mason_options.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/mason2/mason_options.h:51, from /<>/apps/mason2/mason_options.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/mason2/mason_options.h:51, from /<>/apps/mason2/mason_options.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/mason2/mason_options.h:51, from /<>/apps/mason2/mason_options.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/mason2/mason_options.h:51, from /<>/apps/mason2/mason_options.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/mason2/mason_options.h:51, from /<>/apps/mason2/mason_options.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/mason2/mason_options.h:51, from /<>/apps/mason2/mason_options.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -c /<>/apps/mason2/methylation_levels.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/methylation_levels.cpp:35: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/methylation_levels.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/index.h:41, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/methylation_levels.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/methylation_levels.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/methylation_levels.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/index.h:41, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/methylation_levels.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/methylation_levels.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 0%] Built target pair_align_global_1001 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake --color= In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/index.h:41, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/methylation_levels.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/index.h:41, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/methylation_levels.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ Scanning dependencies of target pair_align_global_1111 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp [ 1%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_454.cpp.o -c /<>/apps/mason2/simulate_454.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/index.h:194, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/sequencing.h:49, from /<>/apps/mason2/simulate_454.cpp:35: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_454.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_454.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_454.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_454.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_454.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_454.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_454.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_454.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 1%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_base.cpp.o -c /<>/apps/mason2/simulate_base.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/sequencing.h:49, from /<>/apps/mason2/simulate_base.cpp:35: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_base.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_base.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_base.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_base.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_base.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_base.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_base.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_base.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 1%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -c /<>/apps/mason2/simulate_genome.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/simulate_genome.h:45, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/mason2/simulate_genome.h:44, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/simulate_genome.h:45, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/simulate_genome.h:45, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/mason2/simulate_genome.cpp:106:31: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/mason2/simulate_genome.h:44, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/simulate_genome.h:45, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/simulate_genome.h:45, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/mason2/simulate_genome.h:44, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/simulate_genome.h:45, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/simulate_genome.h:45, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/mason2/simulate_genome.cpp:106:31: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/mason2/simulate_genome.h:44, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/simulate_genome.h:45, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/mason2/simulate_genome.h:44, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/mason2/simulate_genome.h:44, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/simulate_genome.h:45, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/mason2/simulate_genome.cpp:106:31: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/mason2/simulate_genome.h:44, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/simulate_genome.h:45, from /<>/apps/mason2/simulate_genome.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 1%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -c /<>/apps/mason2/simulate_illumina.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/sequencing.h:49, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]’: /<>/apps/mason2/simulate_illumina.cpp:264:56: required from here /<>/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 141 | _cargo() | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/bam_io.h:46, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/modifier/modifier_view.h:98:7: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /<>/apps/mason2/simulate_illumina.cpp:264:64: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/modifier/modifier_string.h:141:20: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]’ /<>/apps/mason2/simulate_illumina.cpp:264:56: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >]’ /<>/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]’ /<>/apps/mason2/simulate_illumina.cpp:193:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /<>/apps/mason2/simulate_illumina.cpp:264:64: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/bam_io.h:46, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_illumina.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 1%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -c /<>/apps/mason2/simulate_sanger.cpp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 1%] Built target pair_align_global_1111 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_1101 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/sequencing.h:49, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]’: /<>/apps/mason2/simulate_sanger.cpp:153:56: required from here /<>/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 141 | _cargo() | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/bam_io.h:46, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/modifier/modifier_view.h:98:7: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /<>/apps/mason2/simulate_sanger.cpp:153:64: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/modifier/modifier_string.h:141:20: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]’ /<>/apps/mason2/simulate_sanger.cpp:153:56: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >]’ /<>/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]’ /<>/apps/mason2/simulate_sanger.cpp:59:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /<>/apps/mason2/simulate_sanger.cpp:153:64: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/bam_io.h:46, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/mason2/sequencing.h:43, from /<>/apps/mason2/simulate_sanger.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 1%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -c /<>/apps/mason2/vcf_materialization.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/mason2/methylation_levels.h:38, from /<>/apps/mason2/genomic_variants.h:52, from /<>/apps/mason2/vcf_materialization.h:44, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/vcf_materialization.h:41, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]’: /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/mason2/vcf_materialization.cpp:167:52: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/mason2/vcf_materialization.h:40, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/vcf_materialization.h:41, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/vcf_materialization.h:41, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/mason2/vcf_materialization.h:40, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/vcf_materialization.h:41, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/vcf_materialization.h:41, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/mason2/vcf_materialization.h:40, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/seq_io.h:45, from /<>/apps/mason2/vcf_materialization.h:41, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/mason2/vcf_materialization.h:40, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/mason2/vcf_materialization.cpp:167:52: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/mason2/vcf_materialization.h:40, from /<>/apps/mason2/vcf_materialization.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 1%] Linking CXX static library libmason_sim.a cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/cmake -P CMakeFiles/mason_sim.dir/cmake_clean_target.cmake cd /<>/obj-x86_64-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_sim.dir/link.txt --verbose=1 /usr/bin/ar qc libmason_sim.a CMakeFiles/mason_sim.dir/external_split_merge.cpp.o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o CMakeFiles/mason_sim.dir/mason_options.cpp.o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o CMakeFiles/mason_sim.dir/simulate_454.cpp.o CMakeFiles/mason_sim.dir/simulate_base.cpp.o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o /usr/bin/ranlib libmason_sim.a make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 1%] Built target mason_sim make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_1011 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 1%] Built target pair_align_global_1101 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_0000 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 1%] Built target pair_align_global_1011 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_0001 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 1%] Built target pair_align_global_0000 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_1110 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 1%] Built target pair_align_global_0001 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_0011 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 1%] Built target pair_align_global_1110 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_0010 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 1%] Built target pair_align_global_0011 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_0101 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target pair_align_global_0010 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_0100 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target pair_align_global_0101 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_1010 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target pair_align_global_0100 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_1100 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target pair_align_global_1010 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_0111 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target pair_align_global_1100 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_0110 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target pair_align_global_0111 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_global_1000 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -c /<>/apps/pair_align/lib/pair_align_global.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /<>/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_global.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target pair_align_global_0110 make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_lcs make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -c /<>/apps/pair_align/lib/pair_align_lcs.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_lcs.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target pair_align_lcs make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/pair_align/lib /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/pair_align/lib /<>/obj-x86_64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_local.dir/DependInfo.cmake --color= Scanning dependencies of target pair_align_local make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -c /<>/apps/pair_align/lib/pair_align_local.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /<>/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /<>/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/modifier.h:47, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/align.h:57, from /<>/apps/pair_align/lib/pair_align_lib.h:41, from /<>/apps/pair_align/lib/pair_align_local.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target pair_align_global_1000 make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/param_chooser /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/param_chooser /<>/obj-x86_64-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake --color= Scanning dependencies of target test_funcs_param_chooser make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/param_chooser && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /<>/apps/param_chooser/test_param_chooser.cpp In file included from /<>/include/seqan/basic/basic_debug.h:52, from /<>/include/seqan/basic.h:49, from /<>/apps/param_chooser/test_param_chooser.cpp:44: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:313:28: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); | ^~~~~~ /<>/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro ‘SEQAN_ASSERT_EQ’ 2048 | (_arg1), # _arg1, \ | ^~~~~ In file included from /<>/include/seqan/index.h:194, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/test_param_chooser.cpp:47: /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_debug.h:52, from /<>/include/seqan/basic.h:49, from /<>/apps/param_chooser/test_param_chooser.cpp:44: /<>/include/seqan/index/index_pizzachili.h:314:48: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); | ^~~~~~ /<>/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro ‘SEQAN_ASSERT’ 2224 | (_arg1), # _arg1)) { \ | ^~~~~ In file included from /<>/include/seqan/index.h:194, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/test_param_chooser.cpp:47: /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/test_param_chooser.cpp:47: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/test_param_chooser.cpp:47: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/test_param_chooser.cpp:47: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/test_param_chooser.cpp:47: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/test_param_chooser.cpp:47: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/test_param_chooser.cpp:47: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/test_param_chooser.cpp:47: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/test_param_chooser.cpp:45: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 2%] Linking CXX executable ../../bin/test_funcs_param_chooser cd /<>/obj-x86_64-linux-gnu/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_funcs_param_chooser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -o ../../bin/test_funcs_param_chooser -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target test_funcs_param_chooser make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/param_chooser /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/param_chooser /<>/obj-x86_64-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake --color= Scanning dependencies of target param_chooser make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/param_chooser && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/param_chooser.dir/param_chooser.cpp.o -c /<>/apps/param_chooser/param_chooser.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/apps/param_chooser/../splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec; seqan::SwiftSemiGlobal = seqan::Tag >]’: /<>/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/apps/param_chooser/../splazers/razers.h:1430:19: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/apps/param_chooser/../splazers/paramChooser.h:32, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::String, seqan::Alloc<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::String, seqan::Alloc<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2245:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/sequence.h:74, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/find/find_base.h:305:34: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:1399:15: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/param_chooser/../splazers/razers.h:1430:19: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/param_chooser/../splazers/razers.h:1431:13: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::String, seqan::Alloc<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::String, seqan::Alloc<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2256:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:1399:15: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/sequence.h:74, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/sequence.h:74, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/apps/param_chooser/../splazers/razers.h:1625:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2239:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:91, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/sequence.h:74, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/apps/param_chooser/../splazers/razers.h:1625:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:91, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/sequence.h:74, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/apps/param_chooser/../splazers/razers.h:1625:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2245:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:91, from /<>/apps/param_chooser/../splazers/razers.h:30, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/sequence.h:74, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/param_chooser/../splazers/razers.h:28, from /<>/apps/param_chooser/../splazers/paramChooser.h:34, from /<>/apps/param_chooser/param_chooser.cpp:39: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFindBeginPatternSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:1414:13: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:1432:19: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/sequence.h:74, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/modifier.h:61, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void; typename seqan::Parameter_::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFindBeginPatternSpec = void]’ /<>/apps/param_chooser/../splazers/razers.h:1437:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/param_chooser/param_chooser.cpp:37: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/sequence.h:74, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Reference > >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:840:14: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/param_chooser/../splazers/razers.h:2047:11: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = int; TSpec = seqan::RazerSSpec; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/param_chooser/../splazers/razers.h:2239:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeSet = seqan::StringSet, seqan::Alloc<> > >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = int; TCounts = int; TSpec = seqan::RazerSSpec]’ /<>/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, seqan::ParamChooserOptions&) [with TError = seqan::String]’ /<>/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(seqan::RazerSOptions&, seqan::ParamChooserOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/param_chooser/param_chooser.cpp:339:43: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/param_chooser/param_chooser.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 2%] Linking CXX executable ../../bin/param_chooser cd /<>/obj-x86_64-linux-gnu/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/param_chooser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/param_chooser.dir/param_chooser.cpp.o -o ../../bin/param_chooser -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target param_chooser make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/rabema /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/rabema /<>/obj-x86_64-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake --color= Scanning dependencies of target rabema_do_search make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_do_search.dir/do_search.cpp.o -c /<>/apps/rabema/do_search.cpp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target pair_align_local make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/rabema /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/rabema /<>/obj-x86_64-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake --color= Scanning dependencies of target rabema_evaluate make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -c /<>/apps/rabema/rabema_evaluate.cpp In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/rabema/do_search.cpp:7: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]’: /<>/include/seqan/modifier/modifier_iterator.h:72:7: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ /<>/apps/rabema/curve_smoothing.h:254:100: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]’ /<>/apps/rabema/curve_smoothing.h:257:79: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/rabema/do_search.cpp:7: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/modifier/modifier_reverse.h:513:97: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]’ /<>/apps/rabema/curve_smoothing.h:257:118: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/rabema/do_search.cpp:7: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/find.h:44, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/find.h:44, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:76, from /<>/include/seqan/find.h:44, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /<>/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /<>/apps/rabema/do_search.cpp:27:89: required from here /<>/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/find.h:44, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/rabema/do_search.cpp:7: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Reference > >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:840:14: required from ‘void seqan::setValue(seqan::Holder >&, const TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /<>/apps/rabema/do_search.cpp:27:89: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/modifier/modifier_reverse.h:625:12: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /<>/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /<>/apps/rabema/do_search.cpp:27:89: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/find.h:43, from /<>/apps/rabema/do_search.cpp:8: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/bam_io.h:50, from /<>/apps/rabema/rabema_evaluate.cpp:29: /<>/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = unsigned int; TCargo = unsigned int]’: /<>/include/seqan/misc/interval_tree.h:1502:18: required from ‘void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2) [with TValue = unsigned int; TCargo = unsigned int; TValue2 = unsigned int]’ /<>/apps/rabema/rabema_evaluate.cpp:644:22: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_evaluate.cpp:1402:85: required from here /<>/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/bam_io.h:50, from /<>/apps/rabema/rabema_evaluate.cpp:29: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/bam_io.h:50, from /<>/apps/rabema/rabema_evaluate.cpp:29: /<>/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/bam_io.h:50, from /<>/apps/rabema/rabema_evaluate.cpp:29: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/bam_io.h:50, from /<>/apps/rabema/rabema_evaluate.cpp:29: /<>/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/bam_io.h:50, from /<>/apps/rabema/rabema_evaluate.cpp:29: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:76, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /<>/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /<>/apps/rabema/rabema_evaluate.cpp:623:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_evaluate.cpp:1402:85: required from here /<>/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /<>/apps/rabema/rabema_evaluate.cpp:623:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_evaluate.cpp:1402:85: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/modifier/modifier_reverse.h:625:12: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /<>/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /<>/apps/rabema/rabema_evaluate.cpp:623:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_evaluate.cpp:1402:85: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_evaluate.cpp:28: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 2%] Linking CXX executable ../../bin/rabema_do_search cd /<>/obj-x86_64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_do_search.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_do_search.dir/do_search.cpp.o -o ../../bin/rabema_do_search -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target rabema_do_search make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/rabema /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/rabema /<>/obj-x86_64-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake --color= Scanning dependencies of target rabema_build_gold_standard make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -c /<>/apps/rabema/rabema_build_gold_standard.cpp In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]’: /<>/include/seqan/modifier/modifier_iterator.h:72:7: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ /<>/apps/rabema/curve_smoothing.h:254:100: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]’ /<>/apps/rabema/curve_smoothing.h:257:79: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/modifier/modifier_reverse.h:513:97: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]’ /<>/apps/rabema/curve_smoothing.h:257:118: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:76, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /<>/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /<>/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /<>/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_build_gold_standard.cpp:1204:105: required from here /<>/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /<>/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /<>/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_build_gold_standard.cpp:1204:105: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/modifier/modifier_reverse.h:625:12: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /<>/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /<>/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /<>/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /<>/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /<>/apps/rabema/rabema_build_gold_standard.cpp:1204:105: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rabema/rabema_build_gold_standard.cpp:35: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 2%] Linking CXX executable ../../bin/rabema_build_gold_standard cd /<>/obj-x86_64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_build_gold_standard.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -o ../../bin/rabema_build_gold_standard -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target rabema_build_gold_standard make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/rabema /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/rabema /<>/obj-x86_64-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake --color= Scanning dependencies of target rabema_prepare_sam make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -c /<>/apps/rabema/prepare_sam.cpp [ 2%] Linking CXX executable ../../bin/rabema_evaluate cd /<>/obj-x86_64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_evaluate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -o ../../bin/rabema_evaluate -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 2%] Built target rabema_evaluate make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/razers /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/razers /<>/obj-x86_64-linux-gnu/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake --color= Scanning dependencies of target razers make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 2%] Building CXX object apps/razers/CMakeFiles/razers.dir/razers.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers.dir/razers.cpp.o -c /<>/apps/razers/razers.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/rabema/prepare_sam.cpp:29: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/rabema/prepare_sam.cpp:29: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/rabema/prepare_sam.cpp:29: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/rabema/prepare_sam.cpp:29: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/rabema/prepare_sam.cpp:29: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/rabema/prepare_sam.cpp:29: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/rabema/prepare_sam.cpp:29: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/bam_io.h:47, from /<>/apps/rabema/prepare_sam.cpp:29: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:194, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers/razers.cpp:622:69: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers/razers.cpp:622:69: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/basic/basic_stream.h:1085:63: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter >, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = seqan::VirtualStream >; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]’ /<>/apps/razers/outputFormat.h:722:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, seqan::CharString, seqan::CharString, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeNames = seqan::StringSet > >; TReads = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadNames = seqan::StringSet > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:232:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers/razers.cpp:622:69: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers/razers.cpp:50: /<>/apps/razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’: /<>/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/apps/razers/razers.h:1471:19: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers/razers.cpp:50: /<>/apps/razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’: /<>/apps/razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/apps/razers/razers.h:1471:19: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers/razers.cpp:622:69: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/index/find_swift.h:396:104: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /<>/apps/razers/razers_matepairs.h:394:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter >, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = seqan::VirtualStream >; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]’ /<>/apps/razers/outputFormat.h:722:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, seqan::CharString, seqan::CharString, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeNames = seqan::StringSet > >; TReads = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadNames = seqan::StringSet > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:232:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers/razers.cpp:622:69: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /<>/apps/razers/razers_matepairs.h:394:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers/razers.h:28, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::String, seqan::Alloc<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::String, seqan::Alloc<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers/razers.h:28, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = void]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/razers/razers.h:1471:19: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/razers/razers.h:1472:13: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2279:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::String, seqan::Alloc<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2279:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = void]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2282:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::String, seqan::Alloc<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = void]’ /<>/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2282:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers/razers.h:28, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long unsigned int]’: /<>/include/seqan/index/find_swift.h:1876:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]’: /<>/include/seqan/index/find_swift.h:1845:48: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers/razers.h:28, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = void]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter >, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = seqan::VirtualStream >; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]’ /<>/apps/razers/outputFormat.h:722:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, seqan::CharString, seqan::CharString, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeNames = seqan::StringSet > >; TReads = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadNames = seqan::StringSet > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:232:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/apps/razers/razers_matepairs.h:375:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:91, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/apps/razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/apps/razers/razers_matepairs.h:375:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:91, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/apps/razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/apps/razers/razers_matepairs.h:375:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:91, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/apps/razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers/razers.h:30, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers/razers.h:28, from /<>/apps/razers/razers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::FindInfix; TFindBeginPatternSpec = void]’ /<>/apps/razers/razers.h:1455:13: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /<>/apps/razers/razers.h:1473:19: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:1845:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/modifier.h:61, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void; typename seqan::Parameter_::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFindBeginPatternSpec = void]’ /<>/apps/razers/razers.h:1478:13: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/razers/razers.h:1971:11: required from ‘int seqan::mapSingleReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/index/index_wotd.h:262:37: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers/razers_matepairs.h:394:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers/razers.cpp:697:84: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers/razers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 3%] Linking CXX executable ../../bin/rabema_prepare_sam cd /<>/obj-x86_64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_prepare_sam.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -o ../../bin/rabema_prepare_sam -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 3%] Built target rabema_prepare_sam make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/razers3 /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/razers3 /<>/obj-x86_64-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake --color= Scanning dependencies of target razers3_quality2prob make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 3%] Building CXX object apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -c /<>/apps/razers3/quality2prob.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/quality2prob.cpp:7: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers3/quality2prob.cpp:42:50: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers3/quality2prob.cpp:42:50: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers3/quality2prob.cpp:42:50: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers3/quality2prob.cpp:42:50: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers3/quality2prob.cpp:42:50: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/quality2prob.cpp:5: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 3%] Linking CXX executable ../../bin/razers3_quality2prob cd /<>/obj-x86_64-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_quality2prob.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -o ../../bin/razers3_quality2prob -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 3%] Built target razers3_quality2prob make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/razers3 /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/razers3 /<>/obj-x86_64-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake --color= Scanning dependencies of target razers3_simulate_reads make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 3%] Building CXX object apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -c /<>/apps/razers3/simulate_reads.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]’ /<>/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]’ /<>/apps/razers3/simulate_reads.cpp:120:53: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]’ /<>/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]’ /<>/apps/razers3/simulate_reads.cpp:120:53: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]’ /<>/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]’ /<>/apps/razers3/simulate_reads.cpp:120:53: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]’ /<>/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]’ /<>/apps/razers3/simulate_reads.cpp:120:53: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]’ /<>/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]’ /<>/apps/razers3/simulate_reads.cpp:120:53: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/razers3/simulate_reads.cpp:6: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 3%] Building CXX object apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers.dir/param_tabs.cpp.o -c /<>/apps/razers/param_tabs.cpp [ 3%] Linking CXX executable ../../bin/razers cd /<>/obj-x86_64-linux-gnu/apps/razers && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers.dir/razers.cpp.o CMakeFiles/razers.dir/param_tabs.cpp.o -o ../../bin/razers -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 3%] Built target razers make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/razers3 /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/razers3 /<>/obj-x86_64-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake --color= Scanning dependencies of target razers3 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 3%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3.dir/razers.cpp.o -c /<>/apps/razers3/razers.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers3/razers.cpp:785:69: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1348:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1348:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1348:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1351:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1351:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1351:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1362:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1362:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:75: /<>/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]’: /<>/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1362:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers3/razers.cpp:785:69: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers3/razers.cpp:785:69: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers3/razers.cpp:785:69: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/stream/tokenization.h:489:11: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]’ /<>/include/seqan/store/store_io.h:740:27: required from ‘void seqan::write(TTarget&, seqan::FragmentStore&, Amos) [with TTarget = seqan::VirtualStream >; TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; seqan::Amos = const seqan::Tag]’ /<>/apps/razers3/outputFormat.h:1222:14: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/store/store_io.h:745:69: required from ‘void seqan::write(TTarget&, seqan::FragmentStore&, Amos) [with TTarget = seqan::VirtualStream >; TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; seqan::Amos = const seqan::Tag]’ /<>/apps/razers3/outputFormat.h:1222:14: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/razers3/razers.cpp:785:69: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’: /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]’: /<>/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::ReverseComplementString::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]’ /<>/include/seqan/store/store_io_sam.h:936:80: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 141 | _cargo() | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]’ /<>/include/seqan/store/store_io.h:740:27: required from ‘void seqan::write(TTarget&, seqan::FragmentStore&, Amos) [with TTarget = seqan::VirtualStream >; TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; seqan::Amos = const seqan::Tag]’ /<>/apps/razers3/outputFormat.h:1222:14: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’: /<>/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/index.h:223, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSpec = void]’: /<>/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = void; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’: /<>/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’: /<>/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/index.h:223, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSpec = seqan::Hamming_]’: /<>/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = seqan::Hamming_; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesNone_]’: /<>/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesNone_]’: /<>/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesNone_]’: /<>/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers3/razers.h:32, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_pigeonhole.h:969:48: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’: /<>/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const seqan::RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/index.h:223, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSpec = void]’: /<>/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = void; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const seqan::RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’: /<>/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const seqan::RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers3/razers.h:32, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:2081:73: required from ‘bool seqan::windowFindBegin(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, unsigned int, TThreadLocalStorages&, const seqan::String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’: /<>/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(seqan::ThreadLocalStorage >&, seqan::Job >&, const seqan::String >&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode; THitString = seqan::String, seqan::Alloc<> >]’ /<>/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(seqan::FragmentStore&, TThreadLocalStorages&, const seqan::String >&, const TContigId&, TCounts&, char, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TContigId = unsigned int; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/index.h:223, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSpec = void]’: /<>/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = void; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’: /<>/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(seqan::ThreadLocalStorage >&, seqan::Job >&, const seqan::String >&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode; THitString = seqan::String, seqan::Alloc<> >]’ /<>/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(seqan::FragmentStore&, TThreadLocalStorages&, const seqan::String >&, const TContigId&, TCounts&, char, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TContigId = unsigned int; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const seqan::RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’: /<>/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const seqan::RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’: /<>/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(seqan::ThreadLocalStorage >&, seqan::Job >&, const seqan::String >&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode; THitString = seqan::String, seqan::Alloc<> >]’ /<>/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(seqan::FragmentStore&, TThreadLocalStorages&, const seqan::String >&, const TContigId&, TCounts&, char, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TContigId = unsigned int; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers3/razers.h:32, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_pigeonhole.h:969:48: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:223, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSpec = seqan::Hamming_]’: /<>/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = seqan::Hamming_; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const seqan::RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers3/razers.h:32, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:2081:73: required from ‘bool seqan::windowFindBegin(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, unsigned int, TThreadLocalStorages&, const seqan::String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:223, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSpec = seqan::Hamming_]’: /<>/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = seqan::Hamming_; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const seqan::RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesNone_]’: /<>/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const seqan::RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesNone_]’: /<>/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const seqan::RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesNone_]’: /<>/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(seqan::ThreadLocalStorage >&, seqan::Job >&, const seqan::String >&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode; THitString = seqan::String, seqan::Alloc<> >]’ /<>/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(seqan::FragmentStore&, TThreadLocalStorages&, const seqan::String >&, const TContigId&, TCounts&, char, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TContigId = unsigned int; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesNone_]’: /<>/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(seqan::ThreadLocalStorage >&, seqan::Job >&, const seqan::String >&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode; THitString = seqan::String, seqan::Alloc<> >]’ /<>/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(seqan::FragmentStore&, TThreadLocalStorages&, const seqan::String >&, const TContigId&, TCounts&, char, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TContigId = unsigned int; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesNone_]’: /<>/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const seqan::RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesNone_]’: /<>/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(seqan::ThreadLocalStorage >&, seqan::Job >&, const seqan::String >&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode; THitString = seqan::String, seqan::Alloc<> >]’ /<>/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(seqan::FragmentStore&, TThreadLocalStorages&, const seqan::String >&, const TContigId&, TCounts&, char, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TContigId = unsigned int; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:74: /<>/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; TDifference = long int]’: /<>/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String, seqan::Alloc<> >; TPosition = long int; TCount = unsigned int]’ /<>/include/seqan/align/gaps_base.h:513:15: required from ‘void seqan::insertGap(seqan::Gaps&, TPosition) [with TSequence = seqan::String, seqan::Alloc<> >; TSpec = seqan::AnchorGaps, seqan::Alloc<> > >; TPosition = long int]’ /<>/include/seqan/store/store_all.h:2067:42: required from ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TScore = seqan::Score >; TShrinkMatches = seqan::True]’ /<>/apps/razers3/outputFormat.h:1221:40: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /<>/apps/razers3/razers_matepairs.h:680:20: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers3/razers.h:32, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_pigeonhole.h:932:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long unsigned int]’: /<>/include/seqan/index/find_pigeonhole.h:941:46: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers3/razers.h:32, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:2088:30: required from ‘bool seqan::windowFindBegin(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, unsigned int, TThreadLocalStorages&, const seqan::String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers3/razers.h:32, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_pigeonhole.h:932:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]’ /<>/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers3/razers.h:32, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:2088:30: required from ‘bool seqan::windowFindBegin(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, unsigned int, TThreadLocalStorages&, const seqan::String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:24: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]’ /<>/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/bam_io/cigar.h:529:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:20: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:24: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]’ /<>/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/bam_io/cigar.h:529:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 94 | : data_iterator(_other.data_iterator) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]’ /<>/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/bam_io/cigar.h:529:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:20: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]’ /<>/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/bam_io/cigar.h:529:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 94 | : data_iterator(_other.data_iterator) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]’ /<>/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/bam_io/cigar.h:534:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:20: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]’ /<>/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/bam_io/cigar.h:534:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 94 | : data_iterator(_other.data_iterator) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >]’ /<>/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]’ /<>/include/seqan/store/store_io_sam.h:811:66: required from ‘void seqan::_fillBamSeqAndQual(TSeq&, TQual&, const TRead&) [with TSeq = seqan::String, seqan::Alloc<> >; TQual = seqan::String >; TRead = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]’ /<>/include/seqan/store/store_io_sam.h:936:31: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/razers3/razers_matepairs_parallel.h:398:24: required from ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_matepairs_parallel.h:1463:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/razers3/razers_parallel.h:859:24: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 3%] Linking CXX executable ../../bin/razers3_simulate_reads cd /<>/obj-x86_64-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_simulate_reads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -o ../../bin/razers3_simulate_reads -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 3%] Built target razers3_simulate_reads make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/rep_sep /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/rep_sep /<>/obj-x86_64-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake --color= Scanning dependencies of target rep_sep make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:24: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]’ /<>/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]’ /<>/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]’ /<>/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/include/seqan/bam_io/cigar.h:534:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/apps/razers3/razers.cpp:63: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ [ 3%] Building CXX object apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/rep_sep && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.1.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o -c /<>/apps/rep_sep/rep_sep.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/apps/razers3/razers_matepairs.h:654:36: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /<>/apps/razers3/razers.h:2241:41: required from ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Pigeonhole; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/apps/razers3/razers.h:2795:64: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = void; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_matepairs.h:1088:24: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/apps/razers3/razers_parallel.h:852:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Pigeonhole; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/apps/razers3/razers_parallel.h:852:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/apps/razers3/razers_matepairs.h:654:36: required from ‘void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/apps/razers3/razers_parallel.h:852:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/razers3/razers.h:32, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_myers_ukkonen.h:989:66: required from ‘bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1181:44: required from ‘bool seqan::_stateInit(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1535:24: required from ‘bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AlignTextBanded; TFindBeginPatternSpec = void]’ /<>/apps/razers3/razers.h:2177:16: required from ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:61, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/basic/iterator_interface.h:430:24: required from ‘void seqan::goEnd(TIterator&) [with TIterator = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/find/find_base.h:737:10: required from ‘void seqan::goEnd(seqan::Finder&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1537:18: required from ‘bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::AlignTextBanded; TFindBeginPatternSpec = void]’ /<>/apps/razers3/razers.h:2245:32: required from ‘bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/apps/razers3/razers.h:2948:40: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Pigeonhole; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/apps/razers3/razers.h:2795:64: required from ‘void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = void; TOptions = seqan::RazerSCoreOptions >]’ /<>/apps/razers3/razers.h:3026:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:223, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:223, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /<>/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/apps/razers3/razers.h:2948:40: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /<>/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:223, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:223, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /<>/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /<>/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/apps/razers3/razers_matepairs_parallel.h:33, from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/gaps_anchor.h:180:26: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/gaps_iterator_anchor.h:169:56: required from ‘typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/basic/proxy_base.h:151:37: required from ‘typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >::Type = char]’ /<>/include/seqan/basic/fundamental_conversion.h:149:23: required from ‘typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; typename seqan::Convert::Type = char]’ /<>/include/seqan/bam_io/cigar.h:241:45: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/gaps_iterator_anchor.h:169:69: required from ‘typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/basic/proxy_base.h:151:37: required from ‘typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >::Type = char]’ /<>/include/seqan/basic/fundamental_conversion.h:149:23: required from ‘typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; typename seqan::Convert::Type = char]’ /<>/include/seqan/bam_io/cigar.h:241:45: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]’ /<>/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]’ /<>/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:650:46: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]’ /<>/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’ /<>/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/gaps_iterator_anchor.h:169:56: required from ‘typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/modifier/modifier_alphabet_expansion.h:357:37: required from ‘typename seqan::Convert >, seqan::Proxy >::Type seqan::convertImpl(seqan::Convert >, T>, const seqan::Proxy&) [with THost = seqan::SimpleType; char CHAR = '-'; TSpec = seqan::Tag; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec2 = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >, seqan::Proxy >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/basic/fundamental_conversion.h:149:23: required from ‘typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >; TSource = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; typename seqan::Convert::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/modifier/modifier_alphabet_expansion.h:92:59: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/gaps_iterator_anchor.h:169:17: required from ‘typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/basic/proxy_base.h:151:37: required from ‘typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >::Type = char]’ /<>/include/seqan/basic/fundamental_conversion.h:149:23: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:994:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]’ /<>/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:631:45: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]’ /<>/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]’ /<>/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/modifier.h:61, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(const seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::ModView > >; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >]’: /<>/include/seqan/modifier/modifier_reverse.h:314:32: required from ‘typename seqan::Position > >::Type seqan::position(const seqan::ModifiedIterator >&) [with THost = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >; typename seqan::Position > >::Type = long unsigned int]’ /<>/include/seqan/align/dp_algorithm_impl.h:675:73: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]’ /<>/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/modifier/modifier_iterator.h:288:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 288 | TContainer cont(container(host(me))); | ^~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:586:12: required from ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/gaps_iterator_anchor.h:169:56: required from ‘typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/basic/proxy_base.h:151:37: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]’ /<>/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:61, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::ModView > >; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >]’: /<>/include/seqan/modifier/modifier_iterator.h:278:30: required from ‘typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]’ /<>/include/seqan/align/dp_algorithm_impl.h:397:81: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::SimpleType; TSeqVValue = seqan::SimpleType; TSeqVIterator = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >; TScoringScheme = seqan::Score >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/align/dp_algorithm_impl.h:891:38: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]’ /<>/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]’ /<>/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/razers3/razers.cpp:62: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’ /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/index/find_pigeonhole.h:318:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’ /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’ /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/index/find_pigeonhole.h:318:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’ /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’ /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]’ /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/razers3/razers.h:34, from /<>/apps/razers3/razers.cpp:74: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]’ /<>/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/apps/razers3/razers.cpp:85: /<>/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]’ /<>/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]’ /<>/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /<>/apps/razers3/razers.cpp:866:66: required from here /<>/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/razers3/razers.cpp:61: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/razers3/razers.cpp:60: /<>/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rep_sep/rep_sep.cpp:27: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rep_sep/rep_sep.cpp:27: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rep_sep/rep_sep.cpp:27: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rep_sep/rep_sep.cpp:27: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rep_sep/rep_sep.cpp:27: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rep_sep/rep_sep.cpp:27: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/rep_sep/rep_sep.cpp:27: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>; TSource = GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/sequence/sequence_interface.h:702:11: required from ‘void seqan::assignValue(T&, TPos, const TValue&) [with T = seqan::String, seqan::AlignedReadStoreElement, void>, long unsigned int>, seqan::Alloc<> >; TValue = GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>; TPos = unsigned int]’ /<>/include/seqan/graph_types/property_map_generic.h:186:16: required from ‘typename seqan::EnableIf >, void>::Type seqan::assignProperty(TPropertyMap&, TDescriptor, TValue) [with TPropertyMap = seqan::String, seqan::AlignedReadStoreElement, void>, long unsigned int>, seqan::Alloc<> >; TDescriptor = unsigned int; TValue = GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>; typename seqan::EnableIf >, void>::Type = void]’ /<>/apps/rep_sep/rgraph_base.h:191:23: required from ‘GraphCargo& registerRead(ReadGraph&, typename ReadGraph::TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; typename ReadGraph::TId = unsigned int]’ /<>/apps/rep_sep/rgraph_construction.h:82:59: required from ‘void construct(ReadGraph&, const seqan::String > >&, const seqan::FragmentStore&, TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = int]’ /<>/apps/rep_sep/rep_sep.cpp:217:60: required from here /<>/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>& GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>::operator=(const GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/apps/rep_sep/rgraph.h:32, from /<>/apps/rep_sep/rep_sep.cpp:34: /<>/apps/rep_sep/rgraph_base.h:44:5: note: because ‘GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>’ has user-provided ‘GraphCargo::GraphCargo(const GraphCargo&) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int]’ 44 | GraphCargo(GraphCargo const& other) | ^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rep_sep/rep_sep.cpp:27: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/rep_sep/rep_sep.cpp:27: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 4%] Linking CXX executable ../../bin/rep_sep cd /<>/obj-x86_64-linux-gnu/apps/rep_sep && /usr/bin/cmake -E cmake_link_script CMakeFiles/rep_sep.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rep_sep.dir/rep_sep.cpp.o -o ../../bin/rep_sep -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target rep_sep make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/sak /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/sak /<>/obj-x86_64-linux-gnu/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake --color= Scanning dependencies of target sak make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 4%] Building CXX object apps/sak/CMakeFiles/sak.dir/sak.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/sak && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sak.dir/sak.cpp.o -c /<>/apps/sak/sak.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/sak/sak.cpp:337:62: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/sak/sak.cpp:337:62: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/sak/sak.cpp:337:62: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/sak/sak.cpp:347:59: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/stream/tokenization.h:489:11: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]’ /<>/include/seqan/seq_io/fasta_fastq.h:468:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]’ /<>/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]’ /<>/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]’ /<>/apps/sak/sak.cpp:424:110: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /<>/include/seqan/stream/tokenization.h:489:11: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment >, seqan::InfixSegment>; TSize = int]’ /<>/include/seqan/seq_io/fasta_fastq.h:475:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]’ /<>/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]’ /<>/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]’ /<>/apps/sak/sak.cpp:424:110: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/sak/sak.cpp:337:62: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]’ /<>/include/seqan/seq_io/fasta_fastq.h:468:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]’ /<>/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]’ /<>/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]’ /<>/apps/sak/sak.cpp:424:110: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment >, seqan::InfixSegment>; TSize = int]’ /<>/include/seqan/seq_io/fasta_fastq.h:475:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]’ /<>/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]’ /<>/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]’ /<>/apps/sak/sak.cpp:424:110: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]’ /<>/include/seqan/seq_io/fasta_fastq.h:468:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]’ /<>/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]’ /<>/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]’ /<>/apps/sak/sak.cpp:424:110: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment >, seqan::InfixSegment>; TSize = int]’ /<>/include/seqan/seq_io/fasta_fastq.h:475:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]’ /<>/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]’ /<>/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]’ /<>/apps/sak/sak.cpp:424:110: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/sak/sak.cpp:42: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 4%] Linking CXX executable ../../bin/sak cd /<>/obj-x86_64-linux-gnu/apps/sak && /usr/bin/cmake -E cmake_link_script CMakeFiles/sak.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sak.dir/sak.cpp.o -o ../../bin/sak -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target sak make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/sam2matrix /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/sam2matrix /<>/obj-x86_64-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake --color= Scanning dependencies of target sam2matrix make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 4%] Building CXX object apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/sam2matrix && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -c /<>/apps/sam2matrix/sam2matrix.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/sam2matrix/sam2matrix.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]’ /<>/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/sam2matrix/sam2matrix.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/sam2matrix/sam2matrix.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]’ /<>/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/sam2matrix/sam2matrix.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/sam2matrix/sam2matrix.cpp:42: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/sam2matrix/sam2matrix.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]’ /<>/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/sam2matrix/sam2matrix.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]’ /<>/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/sam2matrix/sam2matrix.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]’ /<>/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/sam2matrix/sam2matrix.cpp:42: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/sam2matrix/sam2matrix.cpp:43: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 4%] Linking CXX executable ../../bin/sam2matrix cd /<>/obj-x86_64-linux-gnu/apps/sam2matrix && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam2matrix.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -o ../../bin/sam2matrix -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target sam2matrix make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/samcat /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/samcat /<>/obj-x86_64-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake --color= Scanning dependencies of target samcat make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 4%] Building CXX object apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/samcat && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/samcat.dir/samcat.cpp.o -c /<>/apps/samcat/samcat.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/samcat/samcat.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/samcat/samcat.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/samcat/samcat.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/bam_io.h:49, from /<>/apps/samcat/samcat.cpp:37: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/samcat/samcat.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/bam_io.h:47, from /<>/apps/samcat/samcat.cpp:37: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/samcat/samcat.cpp:36: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/samcat/samcat.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 4%] Linking CXX executable ../../bin/samcat cd /<>/obj-x86_64-linux-gnu/apps/samcat && /usr/bin/cmake -E cmake_link_script CMakeFiles/samcat.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/samcat.dir/samcat.cpp.o -o ../../bin/samcat -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target samcat make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/searchjoin /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/searchjoin /<>/obj-x86_64-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake --color= Scanning dependencies of target s4_join make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 4%] Building CXX object apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/searchjoin && /usr/bin/c++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/s4_join.dir/join.cpp.o -c /<>/apps/searchjoin/join.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:319:80: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /<>/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:332:81: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /<>/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:357:80: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /<>/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:370:81: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/join.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /<>/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]’: /<>/include/seqan/basic/basic_stream.h:1085:63: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /<>/apps/searchjoin/writer.h:197:21: required from ‘bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]’ /<>/apps/searchjoin/join.cpp:293:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:311:68: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/find/find_myers_ukkonen.h:1515:50: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:311:68: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’: /<>/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’: /<>/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /<>/include/seqan/find/find_myers_ukkonen.h:1515:50: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:349:68: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’: /<>/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’: /<>/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:311:68: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /<>/apps/searchjoin/writer.h:197:21: required from ‘bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]’ /<>/apps/searchjoin/join.cpp:293:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:311:68: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:349:68: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]’ /<>/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]’ /<>/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]’ /<>/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]’ /<>/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:311:68: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /<>/apps/searchjoin/writer.h:197:21: required from ‘bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]’ /<>/apps/searchjoin/join.cpp:293:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:311:68: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment > >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:349:68: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/join.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String, seqan::Alloc > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String, seqan::Alloc > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String, seqan::Alloc > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String, seqan::Alloc > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:336:88: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:361:87: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:374:88: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /<>/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/join.cpp:323:87: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/join.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/join.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 4%] Linking CXX executable ../../bin/s4_join cd /<>/obj-x86_64-linux-gnu/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/s4_join.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/s4_join.dir/join.cpp.o -o ../../bin/s4_join -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target s4_join make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/searchjoin /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/searchjoin /<>/obj-x86_64-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake --color= Scanning dependencies of target s4_search make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 4%] Building CXX object apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/searchjoin && /usr/bin/c++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/s4_search.dir/search.cpp.o -c /<>/apps/searchjoin/search.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/apps/searchjoin/search.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:282:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/search.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /<>/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:323:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/search.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:282:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/search.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /<>/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:323:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/search.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:405:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/search.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /<>/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:449:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/search.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /<>/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:405:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/apps/searchjoin/search.cpp:61: /<>/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /<>/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:449:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/find/find_myers_ukkonen.h:1515:50: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:508:81: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’: /<>/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’: /<>/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /<>/include/seqan/find/find_myers_ukkonen.h:1515:50: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:536:81: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’: /<>/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/index.h:138, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’: /<>/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]’ /<>/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:508:81: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:536:81: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/index.h:142, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]’ /<>/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]’ /<>/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]’ /<>/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /<>/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]’: /<>/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]’ /<>/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]’ /<>/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]’ /<>/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /<>/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:508:81: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]’: /<>/include/seqan/basic/basic_stream.h:1085:63: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /<>/apps/searchjoin/writer.h:150:17: required from ‘void _write(Writer&, typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /<>/apps/searchjoin/writer.h:98:15: required from ‘void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:142:13: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:508:81: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment > >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]’ /<>/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:536:81: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /<>/apps/searchjoin/writer.h:150:17: required from ‘void _write(Writer&, typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /<>/apps/searchjoin/writer.h:98:15: required from ‘void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:142:13: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:508:81: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/apps/searchjoin/writer.h:132:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/searchjoin/writer.h:98:15: required from ‘void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:142:13: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /<>/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:508:81: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/searchjoin/search.cpp:57: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String, seqan::Alloc > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String, seqan::Alloc > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String, seqan::Alloc > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String, seqan::Alloc > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:524:97: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:544:95: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:552:96: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /<>/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]’ /<>/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]’ /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /<>/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /<>/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /<>/apps/searchjoin/search.cpp:516:96: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/searchjoin/db.h:43, from /<>/apps/searchjoin/search.cpp:61: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/searchjoin/search.cpp:56: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 4%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3.dir/param_tabs.cpp.o -c /<>/apps/razers3/param_tabs.cpp [ 4%] Linking CXX executable ../../bin/razers3 cd /<>/obj-x86_64-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3.dir/razers.cpp.o CMakeFiles/razers3.dir/param_tabs.cpp.o -o ../../bin/razers3 -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target razers3 make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/seqan_tcoffee /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/seqan_tcoffee /<>/obj-x86_64-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake --color= Scanning dependencies of target seqan_tcoffee make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 4%] Building CXX object apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/seqan_tcoffee && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.13.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -c /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/graph_msa.h:40, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = long unsigned int; TCargo = seqan::Pair >]’: /<>/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from ‘void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, long unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >; TScore = long unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = long unsigned int]’ /<>/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from ‘void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, long unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >]’ /<>/include/seqan/graph_msa/graph_align_tcoffee_base.h:191:20: required from ‘void seqan::buildAlignmentGraph(seqan::String&, seqan::Graph >&, FrequencyCounting) [with TFragment = seqan::Fragment<>; TSpec1 = seqan::Alloc<>; TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = long unsigned int; TSpec = seqan::Tag; seqan::FrequencyCounting = const seqan::Tag]’ /<>/include/seqan/graph_msa/graph_align_tcoffee_msa.h:178:24: required from ‘void seqan::evaluateAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:281:26: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here /<>/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1667 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/graph_msa.h:40, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/graph_msa.h:40, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1679 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/graph_msa.h:40, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/graph_msa.h:40, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1701 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/graph_msa.h:40, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_msa.h:37, from /<>/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 4%] Linking CXX executable ../../bin/s4_search cd /<>/obj-x86_64-linux-gnu/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/s4_search.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/s4_search.dir/search.cpp.o -o ../../bin/s4_search -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target s4_search make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/seqcons2 /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/seqcons2 /<>/obj-x86_64-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake --color= Scanning dependencies of target seqcons2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 4%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/seqcons2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons.cpp.o -c /<>/apps/seqcons2/seqcons.cpp [ 4%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_app.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/seqcons2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o -c /<>/apps/seqcons2/seqcons_app.cpp In file included from /<>/include/seqan/index.h:194, from /<>/include/seqan/consensus/overlap_info_computation.h:38, from /<>/include/seqan/consensus.h:65, from /<>/include/seqan/realign.h:48, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; TDifference = long unsigned int]’: /<>/include/seqan/store/store_all.h:1618:57: required from ‘void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]’ /<>/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /<>/apps/seqcons2/seqcons_app.cpp:145:112: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqcons2/seqcons_app.cpp:116:62: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]’ /<>/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /<>/apps/seqcons2/seqcons_app.cpp:145:112: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:20: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]’ /<>/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /<>/apps/seqcons2/seqcons_app.cpp:145:112: required from here /<>/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 94 | : data_iterator(_other.data_iterator) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]’ /<>/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /<>/apps/seqcons2/seqcons_app.cpp:145:112: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:20: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]’ /<>/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /<>/apps/seqcons2/seqcons_app.cpp:145:112: required from here /<>/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 94 | : data_iterator(_other.data_iterator) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/realign.h:55, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/realign/realign_base.h: In instantiation of ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’: /<>/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) | ^~~~ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqcons2/seqcons_app.cpp:116:62: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]’ /<>/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /<>/apps/seqcons2/seqcons_app.cpp:145:112: required from here /<>/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]’ /<>/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /<>/apps/seqcons2/seqcons_app.cpp:145:112: required from here /<>/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqcons2/seqcons_app.cpp:116:62: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]’: /<>/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::ReverseComplementString::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]’ /<>/include/seqan/store/store_io_sam.h:936:80: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:153:32: required from here /<>/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 141 | _cargo() | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/modifier/modifier_view.h:98:7: required from ‘void seqan::_fillBamSeqAndQual(TSeq&, TQual&, const TRead&) [with TSeq = seqan::String, seqan::Alloc<> >; TQual = seqan::String >; TRead = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]’ /<>/include/seqan/store/store_io_sam.h:936:31: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:153:32: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqcons2/seqcons_app.cpp:223:34: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/index.h:223, from /<>/include/seqan/consensus/overlap_info_computation.h:38, from /<>/include/seqan/consensus.h:65, from /<>/include/seqan/realign.h:48, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSpec = void]’: /<>/include/seqan/consensus/overlap_info_computation.h:370:17: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/include/seqan/consensus/overlap_info_computation.h:38, from /<>/include/seqan/consensus.h:65, from /<>/include/seqan/realign.h:48, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; TDifference = unsigned int]’: /<>/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = unsigned int; TTag = seqan::Standard_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/realign/realign_base.h:395:33: required from ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /<>/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/realign/realign_base.h:408:48: required from ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /<>/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:20: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/realign/realign_base.h:408:48: required from ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /<>/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 94 | : data_iterator(_other.data_iterator) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqcons2/seqcons_app.cpp:223:34: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/basic/basic_stream.h:1085:63: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]’ /<>/include/seqan/consensus/overlap_info_computation.h:261:42: required from ‘void seqan::OverlapInfoComputation_::buildGlobalAlignmentOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:161:9: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/include/seqan/index.h:46, from /<>/include/seqan/consensus/overlap_info_computation.h:38, from /<>/include/seqan/consensus.h:65, from /<>/include/seqan/realign.h:48, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole<>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_pigeonhole.h:969:48: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/include/seqan/consensus/overlap_info_computation.h:377:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/consensus/consensus_builder.h:376:20: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/realign/realign_base.h:279:37: required from ‘void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /<>/include/seqan/realign/realign_base.h:1020:13: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:504:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/realign/realign_base.h:280:33: required from ‘void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /<>/include/seqan/realign/realign_base.h:1020:13: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/realign/realign_base.h:408:48: required from ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /<>/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; TDifference = unsigned int]’: /<>/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = unsigned int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = unsigned int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String, seqan::Alloc<> >; TPosition = unsigned int; TCount = unsigned int]’ /<>/include/seqan/realign/realign_base.h:930:19: required from ‘void seqan::AnsonMyersRealigner_::_endContig(unsigned int) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:697:5: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >]’ /<>/include/seqan/bam_io/cigar.h:572:29: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, seqan::BamAlignFunctorDefault&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int]’ /<>/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:153:32: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:20: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >]’ /<>/include/seqan/bam_io/cigar.h:572:29: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, seqan::BamAlignFunctorDefault&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int]’ /<>/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:153:32: required from here /<>/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 94 | : data_iterator(_other.data_iterator) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/modifier/modifier_string.h:141:20: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]’ /<>/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::ReverseComplementString::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]’ /<>/include/seqan/store/store_io_sam.h:936:80: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:153:32: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/index/find_pigeonhole.h:229:32: required from ‘seqan::Finder >::Finder(THaystack&) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /<>/include/seqan/consensus/overlap_info_computation.h:376:23: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/include/seqan/index.h:46, from /<>/include/seqan/consensus/overlap_info_computation.h:38, from /<>/include/seqan/consensus.h:65, from /<>/include/seqan/realign.h:48, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole<>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_pigeonhole.h:932:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/include/seqan/consensus/overlap_info_computation.h:377:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long unsigned int]’: /<>/include/seqan/index/find_pigeonhole.h:941:46: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/include/seqan/consensus/overlap_info_computation.h:377:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = long unsigned int; TCargo = seqan::Pair >]’: /<>/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from ‘void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSetSpec = seqan::Dependent >; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = long unsigned int]’ /<>/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from ‘void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSetSpec = seqan::Dependent >]’ /<>/include/seqan/graph_msa/graph_align_tcoffee_base.h:136:20: required from ‘void seqan::buildAlignmentGraph(seqan::String&, seqan::String&, seqan::Graph >&, FractionalScore) [with TFragment = seqan::Fragment<>; TSpec1 = seqan::Alloc<>; TScoreValue = int; TSpec2 = seqan::Alloc<>; TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >; TCargo = unsigned int; TSpec = seqan::Tag; seqan::FractionalScore = const seqan::Tag]’ /<>/include/seqan/graph_msa/graph_align_tcoffee_base.h:272:24: required from ‘void seqan::buildAlignmentGraph(seqan::String&, seqan::String&, seqan::Graph >&, const TScore&, ReScore) [with TFragment = seqan::Fragment<>; TSpec1 = seqan::Alloc<>; TScoreValue = int; TSpec2 = seqan::Alloc<>; TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >; TCargo = unsigned int; TSpec = seqan::Tag; TScore = seqan::Score >; seqan::ReScore = const seqan::Tag]’ /<>/include/seqan/consensus/consensus_builder.h:384:24: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1667 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1679 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1701 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/graph_align.h:56, from /<>/include/seqan/align.h:59, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; TDifference = long int]’: /<>/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String, seqan::Alloc<> >; TPosition = long int; TCount = unsigned int]’ /<>/include/seqan/consensus/consensus_builder.h:295:23: required from ‘bool seqan::alignmentGraphToFragmentStore(TFragmentStore&, const seqan::Graph, TCargo, TSpec> >&, const seqan::Graph >&, const seqan::String >&, const seqan::String >&, unsigned int, bool) [with TFragmentStore = seqan::FragmentStore<>; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TCargo = unsigned int; TSetSpec = seqan::Dependent >; TSpec = seqan::Tag]’ /<>/include/seqan/consensus/consensus_builder.h:427:34: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TSpec = seqan::GapsIterator, seqan::Alloc<> > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > > > >]’ /<>/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >]’ /<>/include/seqan/bam_io/cigar.h:572:29: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, seqan::BamAlignFunctorDefault&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int]’ /<>/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorDefault]’ /<>/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:153:32: required from here /<>/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/consensus/overlap_info_computation.h:352:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/consensus/consensus_builder.h:376:20: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/consensus/consensus_builder.h:376:20: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/gaps_iterator_anchor.h:162:56: required from ‘typename seqan::Source > > >::Type seqan::source(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/gaps_iterator_anchor.h:183:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/align/gaps_base.h:950:54: required from ‘void seqan::write(TTarget&, const seqan::Gaps&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps, seqan::Alloc<> > >]’ /<>/include/seqan/align/gaps_base.h:965:10: required from ‘TTarget& seqan::operator<<(TTarget&, const seqan::Gaps&) [with TTarget = std::basic_ostream; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps, seqan::Alloc<> > >]’ /<>/include/seqan/realign/realign_base.h:363:40: required from ‘void seqan::AnsonMyersRealignmentRound_::_computeReadClippingInfo(seqan::WindowClippingInfo_&, const TAlignedReadElement&, unsigned int, unsigned int) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /<>/include/seqan/realign/realign_base.h:1067:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/align.h:90, from /<>/include/seqan/store.h:38, from /<>/include/seqan/realign.h:47, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; TDifference = int]’: /<>/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String, seqan::Alloc<> >; TPosition = int; TCount = unsigned int]’ /<>/include/seqan/align/gaps_base.h:513:15: required from ‘void seqan::insertGap(seqan::Gaps&, TPosition) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps, seqan::Alloc<> > >; TPosition = int]’ /<>/include/seqan/realign/realign_base.h:1610:30: required from ‘void seqan::AnsonMyersRealignmentRound_::_updateAlignments(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::Gaps::Type>::Type>::Type> > >&, seqan::Gaps::Type>&, seqan::ExtractProfileInfo_&, const seqan::WindowClippingInfo_&, const TAlignedReadIter&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; typename seqan::BaseAlphabet::Type>::Type>::Type = seqan::SimpleType; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::AnsonMyersRealignmentRound_::TAlignedReadIter = seqan::AlignedReadStoreElement, void>*]’ /<>/include/seqan/realign/realign_base.h:1321:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; TDifference = long int]’: /<>/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String, seqan::Alloc<> >; TPosition = long int; TCount = long int]’ /<>/include/seqan/store/store_all.h:2236:27: required from ‘void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long int; TSize = long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ /<>/include/seqan/store/store_all.h:2321:40: required from ‘void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps, seqan::Alloc<> >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ /<>/include/seqan/store/store_all.h:2437:31: required from ‘void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ /<>/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]’ /<>/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqcons2/seqcons_app.cpp:261:37: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/index/find_pigeonhole.h:229:32: required from ‘seqan::Finder >::Finder(THaystack&) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /<>/include/seqan/consensus/overlap_info_computation.h:376:23: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/gaps_iterator_anchor.h:162:17: required from ‘typename seqan::Source > > >::Type seqan::source(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/gaps_iterator_anchor.h:183:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]’ /<>/include/seqan/align/gaps_base.h:950:54: required from ‘void seqan::write(TTarget&, const seqan::Gaps&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps, seqan::Alloc<> > >]’ /<>/include/seqan/align/gaps_base.h:965:10: required from ‘TTarget& seqan::operator<<(TTarget&, const seqan::Gaps&) [with TTarget = std::basic_ostream; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps, seqan::Alloc<> > >]’ /<>/include/seqan/realign/realign_base.h:363:40: required from ‘void seqan::AnsonMyersRealignmentRound_::_computeReadClippingInfo(seqan::WindowClippingInfo_&, const TAlignedReadElement&, unsigned int, unsigned int) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /<>/include/seqan/realign/realign_base.h:1067:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/gaps_anchor.h:169:26: required from ‘seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/store/store_all.h:2393:29: required from ‘void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ /<>/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]’ /<>/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/seqcons2/seqcons_app.cpp:261:37: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/consensus/overlap_info_computation.h:352:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/consensus/overlap_info_computation.h:352:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Pigeonhole<>; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/index/find_pigeonhole.h:463:41: required from ‘void seqan::_patternInit(seqan::Pattern >&, TFloat) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSpec = void]’ /<>/include/seqan/consensus/overlap_info_computation.h:370:17: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/include/seqan/consensus/overlap_info_computation.h:38, from /<>/include/seqan/consensus.h:65, from /<>/include/seqan/realign.h:48, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = const seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/include/seqan/consensus/overlap_info_computation.h:38, from /<>/include/seqan/consensus.h:65, from /<>/include/seqan/realign.h:48, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(seqan::ConsensusBuilder_::TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; seqan::ConsensusBuilder_::TFragments = seqan::String >]’ /<>/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(seqan::ConsensusBuilder_::TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; seqan::ConsensusBuilder_::TFragments = seqan::String >]’ /<>/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(seqan::ConsensusBuilder_::TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; seqan::ConsensusBuilder_::TFragments = seqan::String >]’ /<>/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(seqan::ConsensusBuilder_::TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; seqan::ConsensusBuilder_::TFragments = seqan::String >]’ /<>/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:296:40: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:382:27: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/align/dp_algorithm_impl.h:453:18: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/align/dp_algorithm_impl.h:515:18: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::String >, seqan::Alloc<> >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >, seqan::Score > > >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::String >, seqan::Alloc<> >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >, seqan::Score > > >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::String >, seqan::Alloc<> >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::WeightedConsensusScore >, seqan::Score > >; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/realign/realign_base.h:639:20: required from ‘void seqan::_readToProfileAlignment(TProfileGaps&, TReadGaps&, const TConsensusScore&, const TAlignConfig&, int&, int&, const TAlgoTag&) [with TProfileGaps = seqan::Gaps >, seqan::Alloc<> >, seqan::Tag >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TConsensusScore = seqan::Score >, seqan::Score > > >; TAlignConfig = seqan::AlignConfig; TAlgoTag = seqan::Tag]’ /<>/include/seqan/realign/realign_base.h:657:36: required from ‘void seqan::_readToProfileAlignment(TProfileGaps&, TReadGaps&, const TConsensusScore&, const TAlignConfig&, int&, int&, bool) [with TProfileGaps = seqan::Gaps >, seqan::Alloc<> >, seqan::Tag >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TConsensusScore = seqan::Score >, seqan::Score > > >; TAlignConfig = seqan::AlignConfig]’ /<>/include/seqan/realign/realign_base.h:1209:36: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /<>/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]’ /<>/apps/seqcons2/seqcons_app.cpp:314:108: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/realign.h:45, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/realign.h:44, from /<>/apps/seqcons2/seqcons_app.cpp:40: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ [ 4%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_options.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/seqcons2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -c /<>/apps/seqcons2/seqcons_options.cpp [ 4%] Linking CXX executable ../../bin/seqan_tcoffee cd /<>/obj-x86_64-linux-gnu/apps/seqan_tcoffee && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqan_tcoffee.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -o ../../bin/seqan_tcoffee -lrt -lz -lbz2 [ 4%] Linking CXX executable ../../bin/seqcons2 cd /<>/obj-x86_64-linux-gnu/apps/seqcons2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqcons2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/seqcons2.dir/seqcons.cpp.o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -o ../../bin/seqcons2 -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 4%] Built target seqan_tcoffee make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/sgip /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/sgip /<>/obj-x86_64-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake --color= Scanning dependencies of target sgip make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object apps/sgip/CMakeFiles/sgip.dir/sgip.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/sgip && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sgip.dir/sgip.cpp.o -c /<>/apps/sgip/sgip.cpp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target seqcons2 make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/snp_store /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/snp_store /<>/obj-x86_64-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake --color= Scanning dependencies of target snp_store make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/snp_store && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/snp_store.dir/snp_store.cpp.o -c /<>/apps/snp_store/snp_store.cpp In file included from /<>/include/seqan/index.h:194, from /<>/include/seqan/consensus/overlap_info_computation.h:38, from /<>/include/seqan/consensus.h:65, from /<>/apps/snp_store/snp_store.cpp:35: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:54, from /<>/include/seqan/basic.h:98, from /<>/include/seqan/sequence.h:74, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/basic/pair_base.h: In instantiation of ‘seqan::Pair::Pair(const T1&, const T2&) [with T1 = unsigned int; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’: /<>/apps/snp_store/snp_store.h:5148:46: required from ‘void seqan::dumpShortIndelPolymorphismsBatch(TFragmentStore&, TReadCigars&, TGenome&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TReadCigars = seqan::StringSet > >; TGenome = seqan::String, seqan::Alloc<> >; TGenomeName = seqan::String >; TFile = std::basic_ofstream; TOptions = seqan::SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /<>/apps/snp_store/snp_store.cpp:971:74: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /<>/apps/snp_store/snp_store.cpp:1412:36: required from here /<>/include/seqan/basic/pair_base.h:120:59: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 120 | Pair(T1 const & _i1, T2 const & _i2) : i1(_i1), i2(_i2) {} | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/snp_store/snp_store.cpp:33: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/snp_store/snp_store.cpp:32: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/snp_store/snp_store.cpp:33: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/snp_store/snp_store.cpp:32: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/snp_store/snp_store.cpp:33: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /<>/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /<>/apps/snp_store/snp_store.cpp:1412:36: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/snp_store/snp_store.cpp:32: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/align.h:90, from /<>/apps/snp_store/snp_store.cpp:33: /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; TDifference = long int]’: /<>/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/apps/snp_store/snp_store.h:4057:36: required from ‘void seqan::dumpVariantsRealignBatch(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TReadCounts = seqan::String >; TReadCigars = seqan::StringSet > >; TGenomeName = seqan::String >; TFile = std::basic_ofstream; TOptions = seqan::SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /<>/apps/snp_store/snp_store.h:2477:41: required from ‘void seqan::dumpVariantsRealignBatchWrap(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TReadCigars = seqan::StringSet > >; TReadCounts = seqan::String >; TGenomeName = seqan::String >; TFile = std::basic_ofstream; TOptions = seqan::SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /<>/apps/snp_store/snp_store.cpp:986:53: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /<>/apps/snp_store/snp_store.cpp:1412:36: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/snp_store/snp_store.cpp:33: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /<>/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /<>/apps/snp_store/snp_store.cpp:1412:36: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/snp_store/snp_store.cpp:32: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/align.h:90, from /<>/apps/snp_store/snp_store.cpp:33: /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors = seqan::String, seqan::Alloc<> >; TDifference = long int]’: /<>/include/seqan/sequence/sequence_interface.h:689:35: required from ‘typename seqan::Iterator >::Type seqan::iter(const T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/sequence/sequence_interface.h:669:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(const T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TPos = long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ /<>/include/seqan/align/gaps_anchor.h:451:22: required from ‘bool seqan::isGap(const seqan::Gaps >&, TPosition) [with TSequence = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String, seqan::Alloc<> >; TPosition = long int]’ /<>/apps/snp_store/snp_store.h:4418:72: required from ‘void seqan::dumpVariantsRealignBatch(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TReadCounts = seqan::String >; TReadCigars = seqan::StringSet > >; TGenomeName = seqan::String >; TFile = std::basic_ofstream; TOptions = seqan::SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /<>/apps/snp_store/snp_store.h:2477:41: required from ‘void seqan::dumpVariantsRealignBatchWrap(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TReadCigars = seqan::StringSet > >; TReadCounts = seqan::String >; TGenomeName = seqan::String >; TFile = std::basic_ofstream; TOptions = seqan::SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /<>/apps/snp_store/snp_store.cpp:986:53: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /<>/apps/snp_store/snp_store.cpp:1412:36: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/snp_store/snp_store.cpp:33: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /<>/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /<>/apps/snp_store/snp_store.cpp:1412:36: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/snp_store/snp_store.cpp:32: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/snp_store/snp_store.cpp:33: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /<>/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /<>/apps/snp_store/snp_store.cpp:1412:36: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/snp_store/snp_store.cpp:32: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/graph_align.h:45, from /<>/include/seqan/align.h:59, from /<>/apps/snp_store/snp_store.cpp:33: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /<>/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /<>/apps/snp_store/snp_store.cpp:1412:36: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/snp_store/snp_store.cpp:31: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/apps/snp_store/snp_store.cpp:32: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 5%] Linking CXX executable ../../bin/sgip cd /<>/obj-x86_64-linux-gnu/apps/sgip && /usr/bin/cmake -E cmake_link_script CMakeFiles/sgip.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sgip.dir/sgip.cpp.o -o ../../bin/sgip -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target sgip make -f apps/splazers/CMakeFiles/splazers.dir/build.make apps/splazers/CMakeFiles/splazers.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/splazers /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/splazers /<>/obj-x86_64-linux-gnu/apps/splazers/CMakeFiles/splazers.dir/DependInfo.cmake --color= Scanning dependencies of target splazers make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/splazers/CMakeFiles/splazers.dir/build.make apps/splazers/CMakeFiles/splazers.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object apps/splazers/CMakeFiles/splazers.dir/splazers.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/splazers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/splazers.dir/splazers.cpp.o -c /<>/apps/splazers/splazers.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]’: /<>/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::ReverseComplementString::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]’ /<>/apps/splazers/outputFormat.h:1591:40: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, seqan::CharString, seqan::CharString, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeNames = seqan::StringSet > >; TReads = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = seqan::String > > >; TReadNames = seqan::StringSet > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 141 | _cargo() | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/basic/basic_stream.h:1085:63: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter >, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = seqan::VirtualStream >; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]’ /<>/apps/splazers/outputFormat.h:900:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, seqan::CharString, seqan::CharString, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeNames = seqan::StringSet > >; TReads = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = seqan::String > > >; TReadNames = seqan::StringSet > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/splazers/splazers.cpp:62: /<>/apps/splazers/razers_spliced.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal, TSufPrefSpec) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec<>; TSufPrefSpec = seqan::LongestSuffix; seqan::SwiftSemiGlobal = seqan::Tag >]’: /<>/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/apps/splazers/razers_spliced.h:666:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 666 | TGenomeInfix oriInf = inf; | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/splazers/splazers.cpp:62: /<>/apps/splazers/razers_spliced.h:674:19: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 674 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/splazers/splazers.cpp:62: /<>/apps/splazers/razers_spliced.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal, TSufPrefSpec) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec<>; TSufPrefSpec = seqan::LongestPrefix; seqan::SwiftSemiGlobal = seqan::Tag >]’: /<>/apps/splazers/razers_spliced.h:2591:20: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/apps/splazers/razers_spliced.h:666:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 666 | TGenomeInfix oriInf = inf; | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/splazers/splazers.cpp:62: /<>/apps/splazers/razers_spliced.h:674:19: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 674 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/splazers/splazers.cpp:50: /<>/apps/splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’: /<>/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/apps/splazers/razers.h:1430:19: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/splazers/splazers.cpp:50: /<>/apps/splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’: /<>/apps/splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers.h:1979:19: required from ‘int seqan::mapSingleReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2125:24: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/apps/splazers/razers.h:1430:19: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/modifier/modifier_string.h:141:20: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]’ /<>/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::ReverseComplementString::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]’ /<>/apps/splazers/outputFormat.h:1591:40: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, seqan::CharString, seqan::CharString, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeNames = seqan::StringSet > >; TReads = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = seqan::String > > >; TReadNames = seqan::StringSet > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/index/find_swift.h:396:104: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /<>/apps/splazers/razers_spliced.h:2419:16: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/index/find_swift.h:396:104: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /<>/apps/splazers/razers_matepairs.h:671:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter >, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = seqan::VirtualStream >; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]’ /<>/apps/splazers/outputFormat.h:900:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, seqan::CharString, seqan::CharString, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeNames = seqan::StringSet > >; TReads = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = seqan::String > > >; TReadNames = seqan::StringSet > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/splazers/razers.h:604:26: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /<>/apps/splazers/razers_spliced.h:2419:16: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3041:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3043:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = void]’ /<>/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/splazers/razers_spliced.h:674:19: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal, TSufPrefSpec) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec<>; TSufPrefSpec = seqan::LongestSuffix; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3074:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = void]’ /<>/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3076:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /<>/apps/splazers/razers_matepairs.h:671:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2187:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2190:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = void]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/splazers/razers.h:1430:19: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2198:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/index.h:222, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]’: /<>/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = void]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2201:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long unsigned int]’: /<>/include/seqan/index/find_swift.h:1876:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(const seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_base.h:910:21: required from ‘typename seqan::Parameter_::Type>::Type seqan::haystack(const TObject&) [with TObject = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; typename seqan::Parameter_::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/index/find_swift.h:1682:38: required from ‘seqan::Pair > >::Type> seqan::positionRange(const seqan::Finder >&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >; typename seqan::Position > >::Type = long unsigned int]’ /<>/include/seqan/index/find_swift.h:1693:25: required from ‘seqan::Pair > >::Type> seqan::positionRange(seqan::Finder >&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >; typename seqan::Position > >::Type = long unsigned int]’ /<>/apps/splazers/razers_spliced.h:2489:26: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:606:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 606 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = void]’ /<>/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(const seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_base.h:910:21: required from ‘typename seqan::Parameter_::Type>::Type seqan::haystack(const TObject&) [with TObject = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; typename seqan::Parameter_::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/index/find_swift.h:1682:38: required from ‘seqan::Pair > >::Type> seqan::positionRange(const seqan::Finder >&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >; typename seqan::Position > >::Type = long unsigned int]’ /<>/include/seqan/index/find_swift.h:1693:25: required from ‘seqan::Pair > >::Type> seqan::positionRange(seqan::Finder >&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >; typename seqan::Position > >::Type = long unsigned int]’ /<>/apps/splazers/razers_spliced.h:2489:26: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:606:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 606 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long unsigned int]’: /<>/include/seqan/index/find_swift.h:1876:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]’: /<>/include/seqan/index/find_swift.h:1845:48: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = void]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >]’ /<>/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]’ /<>/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]’ /<>/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter >, seqan::StreamIterator > >; TContainer = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/include/seqan/modifier/modifier_string.h:801:10: required from ‘TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = seqan::VirtualStream >; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag]’ /<>/apps/splazers/outputFormat.h:1591:14: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, seqan::CharString, seqan::CharString, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenomeNames = seqan::StringSet > >; TReads = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadRegions = seqan::String > > >; TReadNames = seqan::StringSet > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/apps/splazers/razers_spliced.h:2383:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:91, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/apps/splazers/razers_spliced.h:2384:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3041:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:91, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/apps/splazers/razers_spliced.h:2384:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3043:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:91, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFindBeginPatternSpec = void]’ /<>/apps/splazers/razers_spliced.h:652:13: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal, TSufPrefSpec) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec<>; TSufPrefSpec = seqan::LongestSuffix; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /<>/apps/splazers/razers_spliced.h:675:19: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal, TSufPrefSpec) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec<>; TSufPrefSpec = seqan::LongestSuffix; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/splazers/razers_spliced.h:1717:14: required from ‘bool seqan::combineLeftRight(TMatch&, TMatch&, TRead&, TGenome&, seqan::RazerSOptions&, char, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TRead = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGenome = seqan::String, seqan::Alloc<> >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/splazers/razers_spliced.h:2701:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /<>/apps/splazers/razers_matepairs.h:652:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:91, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /<>/apps/splazers/razers_matepairs.h:652:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2187:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:91, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/index.h:87, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /<>/apps/splazers/razers_matepairs.h:652:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2190:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] In file included from /<>/include/seqan/index.h:91, from /<>/apps/splazers/razers.h:30, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /<>/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/modifier/cyclic_shape.h:41, from /<>/include/seqan/modifier.h:68, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/find.h:55, from /<>/apps/splazers/razers.h:28, from /<>/apps/splazers/splazers.cpp:50: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::FindInfix; TFindBeginPatternSpec = void]’ /<>/apps/splazers/razers.h:1414:13: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /<>/apps/splazers/razers.h:1432:19: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:1845:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/modifier.h:61, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void; typename seqan::Parameter_::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFindBeginPatternSpec = void]’ /<>/apps/splazers/razers_spliced.h:688:13: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal, TSufPrefSpec) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec<>; TSufPrefSpec = seqan::LongestSuffix; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/index/find_swift.h:1845:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]’ /<>/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]’ /<>/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Hamming_]’ /<>/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/modifier.h:61, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void; typename seqan::Parameter_::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; THasState = seqan::True; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, seqan::Pattern >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFindBeginPatternSpec = void]’ /<>/apps/splazers/razers.h:1437:13: required from ‘bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TSpec = seqan::RazerSSpec<>; seqan::SwiftSemiGlobal = seqan::Tag >]’ /<>/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/splazers/razers_spliced.h:2701:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/splazers/razers_spliced.h:2701:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, seqan::TReadRegions&, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TOriReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TReadIndexL = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TReadIndexR = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet_&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&, const TShapeL&, const TShapeR&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShapeL = seqan::Shape, seqan::UngappedShape<0> >; TShapeR = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/index/index_wotd.h:262:37: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/splazers/razers_matepairs.h:671:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, seqan::Pattern >&, seqan::Pattern >&, TVerifier&, TVerifier&, TCounts&, char, seqan::RazerSOptions&) [with TMatches = seqan::String >; TGenome = seqan::String, seqan::Alloc<> >; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSwiftSpec = seqan::Tag >; TVerifier = seqan::String, seqan::Alloc<> >, seqan::Myers > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]’ /<>/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, seqan::RazerSOptions&, const TShape&, seqan::Swift) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TSwiftSpec = seqan::Tag >]’ /<>/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, seqan::StringSet > >&, seqan::StringSet > >&, std::map, unsigned int> >&, TReadSet&, seqan::TReadRegions&, TCounts&, seqan::RazerSOptions&) [with TMatches = seqan::String >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::TReadRegions = seqan::String > > >]’ /<>/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /<>/apps/splazers/splazers.cpp:717:81: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/splazers/splazers.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 5%] Linking CXX executable ../../bin/snp_store cd /<>/obj-x86_64-linux-gnu/apps/snp_store && /usr/bin/cmake -E cmake_link_script CMakeFiles/snp_store.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/snp_store.dir/snp_store.cpp.o -o ../../bin/snp_store -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target snp_store make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/stellar /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/stellar /<>/obj-x86_64-linux-gnu/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake --color= Scanning dependencies of target stellar make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object apps/stellar/CMakeFiles/stellar.dir/stellar.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/stellar && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.4.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/stellar.dir/stellar.cpp.o -c /<>/apps/stellar/stellar.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/stellar/stellar.cpp:25: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /<>/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/apps/stellar/stellar.h:677:33: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h:690:60: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const CharString&, const CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /<>/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /<>/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /<>/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /<>/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /<>/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /<>/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /<>/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/stellar/stellar.cpp:28: /<>/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const CharString&, const CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /<>/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const CharString&, const CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /<>/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /<>/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /<>/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /<>/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /<>/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /<>/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /<>/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /<>/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const CharString&, const CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /<>/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/align.h:190, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScore = seqan::Score >; TDiagonal = int]’: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag; TScore = seqan::Score >; TDiagonal = int; seqan::BandedWatermanEggert = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TAlignSpec = seqan::Tag]’ /<>/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:190, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScore = seqan::Score >; TDiagonal = int]’: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag; TScore = seqan::Score >; TDiagonal = int; seqan::BandedWatermanEggert = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TAlignSpec = seqan::Tag]’ /<>/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:190, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScore = seqan::Score >; TDiagonal = int]’: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag; TScore = seqan::Score >; TDiagonal = int; seqan::BandedWatermanEggert = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TAlignSpec = seqan::Tag]’ /<>/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:190, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScore = seqan::Score >; TDiagonal = int]’: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag; TScore = seqan::Score >; TDiagonal = int; seqan::BandedWatermanEggert = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TAlignSpec = seqan::Tag]’ /<>/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:190, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScore = seqan::Score >; TDiagonal = int]’: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag; TScore = seqan::Score >; TDiagonal = int; seqan::BandedWatermanEggert = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TAlignSpec = seqan::Tag]’ /<>/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:190, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScore = seqan::Score >; TDiagonal = int]’: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag; TScore = seqan::Score >; TDiagonal = int; seqan::BandedWatermanEggert = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TAlignSpec = seqan::Tag]’ /<>/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const CharString&, const CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /<>/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Needle >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/stellar/stellar.cpp:25: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Needle >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/stellar/stellar.cpp:25: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Needle >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/stellar/stellar.cpp:25: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Needle >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/stellar/stellar.cpp:25: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Needle >::Type = seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/stellar/stellar.cpp:25: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:72, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSource = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]’: /<>/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TValue2 = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&]’ /<>/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Host >::Type = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(seqan::Pattern&) [with TNeedle = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >; TSpec = seqan::Swift >; typename seqan::Needle >::Type = seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >]’ /<>/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /<>/include/seqan/index.h:92, from /<>/apps/stellar/stellar.cpp:25: /<>/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TTargetSpec = seqan::Alloc<>; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >&; TSource = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’ /<>/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /<>/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/include/seqan/bam_io.h:50, from /<>/include/seqan/seq_io/bam_sam.h:39, from /<>/include/seqan/seq_io.h:55, from /<>/apps/stellar/stellar.cpp:26: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /<>/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /<>/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /<>/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /<>/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /<>/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TValue2 = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:105, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /<>/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:685:47: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:687:48: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:689:47: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:691:48: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /<>/apps/stellar/stellar.cpp:693:53: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/include/seqan/arg_parse.h:44, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]’ /<>/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /<>/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment >, seqan::InfixSegment>&]’ /<>/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /<>/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /<>/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /<>/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /<>/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /<>/apps/stellar/stellar.cpp:695:48: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/include/seqan/arg_parse.h:46, from /<>/apps/stellar/stellar.cpp:24: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 5%] Linking CXX executable ../../bin/splazers cd /<>/obj-x86_64-linux-gnu/apps/splazers && /usr/bin/cmake -E cmake_link_script CMakeFiles/splazers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/splazers.dir/splazers.cpp.o -o ../../bin/splazers -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target splazers make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/tree_recon /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/tree_recon /<>/obj-x86_64-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake --color= Scanning dependencies of target tree_recon make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object apps/tree_recon/CMakeFiles/tree_recon.dir/tree_recon.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/tree_recon && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/tree_recon.dir/tree_recon.cpp.o -c /<>/apps/tree_recon/tree_recon.cpp [ 5%] Linking CXX executable ../../bin/tree_recon cd /<>/obj-x86_64-linux-gnu/apps/tree_recon && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree_recon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/tree_recon.dir/tree_recon.cpp.o -o ../../bin/tree_recon -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target tree_recon make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/yara /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/yara /<>/obj-x86_64-linux-gnu/apps/yara/CMakeFiles/yara_mapper.dir/DependInfo.cmake --color= Scanning dependencies of target yara_mapper make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object apps/yara/CMakeFiles/yara_mapper.dir/mapper.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/yara && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.9.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DYARA_LARGE_CONTIGS=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/yara_mapper.dir/mapper.cpp.o -c /<>/apps/yara/mapper.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:91: /<>/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:425:42: required from here /<>/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:140, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_position.h:205:36: required from ‘typename seqan::Parameter_::Type seqan::cargo(const seqan::ModifiedString >&) [with THost = seqan::String >, seqan::Alloc<> >; TPositions = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /<>/include/seqan/modifier/modifier_position.h:309:23: required from ‘bool seqan::empty(const seqan::ModifiedString >&) [with THost = seqan::String >, seqan::Alloc<> >; TPositions = seqan::Segment >, seqan::InfixSegment>]’ /<>/apps/yara/mapper.h:858:18: required from ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ /<>/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(seqan::StringSet >&, typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]’: /<>/include/seqan/basic/basic_stream.h:1085:63: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/include/seqan/bam_io/write_sam.h:114:14: required from ‘void seqan::write(TTarget&, const BamHeader&, const seqan::BamIOContext&, const Sam&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TNameStore = seqan::StringSet >, seqan::Owner > > >; TNameStoreCache = seqan::NameStoreCache >, seqan::Owner > > >, seqan::String > >; TStorageSpec = seqan::Dependent >; seqan::BamHeader = seqan::String; seqan::Sam = seqan::Tag]’ /<>/include/seqan/bam_io/bam_file.h:293:14: required from ‘void seqan::write(TTarget&, const BamHeader&, seqan::BamIOContext&, const seqan::TagSelector&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TNameStore = seqan::StringSet >, seqan::Owner > > >; TNameStoreCache = seqan::NameStoreCache >, seqan::Owner > > >, seqan::String > >; TStorageSpec = seqan::Dependent >; TTagList = seqan::TagList >; seqan::BamHeader = seqan::String]’ /<>/include/seqan/bam_io/bam_file.h:295:14: required from ‘void seqan::write(TTarget&, const BamHeader&, seqan::BamIOContext&, const seqan::TagSelector&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TNameStore = seqan::StringSet >, seqan::Owner > > >; TNameStoreCache = seqan::NameStoreCache >, seqan::Owner > > >, seqan::String > >; TStorageSpec = seqan::Dependent >; TTagList = seqan::TagList, seqan::TagList > >; seqan::BamHeader = seqan::String]’ /<>/include/seqan/bam_io/bam_file.h:303:10: required from ‘void seqan::writeHeader(seqan::FormattedFile, seqan::Tag, TSpec>&, const BamHeader&) [with TSpec = seqan::StringSet >, seqan::Owner > > >; seqan::BamHeader = seqan::String]’ /<>/apps/yara/mapper.h:515:16: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/yara/file_prefetched.h:151:13: required from ‘bool seqan::open(seqan::PrefetchedFile >&, const char*) [with TFile = seqan::FormattedFile, seqan::Tag >; TRecords = SeqStore >]’ /<>/apps/yara/mapper.h:408:14: required from ‘void _openReadsImpl(Mapper&, SingleEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; SingleEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:402:19: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; TIntegral = long unsigned int]’: /<>/include/seqan/parallel/parallel_algorithms.h:244:37: required from ‘void seqan::iterate(TContainer&, TFunctor, const seqan::Tag&, seqan::Parallel) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TFunctor = ReadsClassifier, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >; TIterTag = seqan::Rooted_; seqan::Parallel = seqan::Tag]’ /<>/apps/yara/mapper_classifier.h:114:12: required from ‘void _classifyReadsImpl(ReadsClassifier&, Strata) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; Strata = seqan::Tag]’ /<>/apps/yara/mapper_classifier.h:76:27: required from ‘ReadsClassifier::ReadsClassifier(ReadsClassifier::TReadsContext&, ReadsClassifier::THits&, const TSeeds&, const Options&) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; ReadsClassifier::TReadsContext = ReadsContext, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; ReadsClassifier::THits = seqan::String >, seqan::Alloc<> >; ReadsClassifier::TSeeds = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >, seqan::Segment, seqan::Alloc<> >, seqan::Owner > > > >]’ /<>/apps/yara/mapper.h:656:17: required from ‘void classifyReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1288:18: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag]’: /<>/include/seqan/parallel/parallel_algorithms.h:244:14: required from ‘void seqan::iterate(TContainer&, TFunctor, const seqan::Tag&, seqan::Parallel) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TFunctor = ReadsClassifier, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >; TIterTag = seqan::Rooted_; seqan::Parallel = seqan::Tag]’ /<>/apps/yara/mapper_classifier.h:114:12: required from ‘void _classifyReadsImpl(ReadsClassifier&, Strata) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; Strata = seqan::Tag]’ /<>/apps/yara/mapper_classifier.h:76:27: required from ‘ReadsClassifier::ReadsClassifier(ReadsClassifier::TReadsContext&, ReadsClassifier::THits&, const TSeeds&, const Options&) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; ReadsClassifier::TReadsContext = ReadsContext, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; ReadsClassifier::THits = seqan::String >, seqan::Alloc<> >; ReadsClassifier::TSeeds = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >, seqan::Segment, seqan::Alloc<> >, seqan::Owner > > > >]’ /<>/apps/yara/mapper.h:656:17: required from ‘void classifyReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1288:18: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_smart_pointer.h:47, from /<>/include/seqan/basic/basic_allocator.h:46, from /<>/include/seqan/basic.h:74, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(seqan::StringSet >&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(seqan::StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>; TKeyGetter = seqan::Getter >, const seqan::Tag >; TMaxKey = long unsigned int; TThreading = seqan::Tag]’ /<>/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /<>/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned int, long unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /<>/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:365:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:386:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/yara/file_prefetched.h:151:13: required from ‘bool seqan::open(seqan::PrefetchedFile >&, const char*) [with TFile = seqan::FormattedFile, seqan::Tag >; TRecords = SeqStore >]’ /<>/apps/yara/mapper.h:408:14: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]’ /<>/include/seqan/parallel/parallel_algorithms.h:244:24: required from ‘void seqan::iterate(TContainer&, TFunctor, const seqan::Tag&, seqan::Parallel) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TFunctor = ReadsClassifier, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >; TIterTag = seqan::Rooted_; seqan::Parallel = seqan::Tag]’ /<>/apps/yara/mapper_classifier.h:114:12: required from ‘void _classifyReadsImpl(ReadsClassifier&, Strata) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; Strata = seqan::Tag]’ /<>/apps/yara/mapper_classifier.h:76:27: required from ‘ReadsClassifier::ReadsClassifier(ReadsClassifier::TReadsContext&, ReadsClassifier::THits&, const TSeeds&, const Options&) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; ReadsClassifier::TReadsContext = ReadsContext, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; ReadsClassifier::THits = seqan::String >, seqan::Alloc<> >; ReadsClassifier::TSeeds = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >, seqan::Segment, seqan::Alloc<> >, seqan::Owner > > > >]’ /<>/apps/yara/mapper.h:656:17: required from ‘void classifyReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1288:18: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/include/seqan/bam_io/write_sam.h:114:14: required from ‘void seqan::write(TTarget&, const BamHeader&, const seqan::BamIOContext&, const Sam&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TNameStore = seqan::StringSet >, seqan::Owner > > >; TNameStoreCache = seqan::NameStoreCache >, seqan::Owner > > >, seqan::String > >; TStorageSpec = seqan::Dependent >; seqan::BamHeader = seqan::String; seqan::Sam = seqan::Tag]’ /<>/include/seqan/bam_io/bam_file.h:293:14: required from ‘void seqan::write(TTarget&, const BamHeader&, seqan::BamIOContext&, const seqan::TagSelector&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TNameStore = seqan::StringSet >, seqan::Owner > > >; TNameStoreCache = seqan::NameStoreCache >, seqan::Owner > > >, seqan::String > >; TStorageSpec = seqan::Dependent >; TTagList = seqan::TagList >; seqan::BamHeader = seqan::String]’ /<>/include/seqan/bam_io/bam_file.h:295:14: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/yara/file_prefetched.h:151:13: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:577:12: required from ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; TIntegral = long unsigned int]’ /<>/include/seqan/parallel/parallel_algorithms.h:244:37: required from ‘void seqan::iterate(TContainer&, TFunctor, const seqan::Tag&, seqan::Parallel) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TFunctor = ReadsClassifier, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >; TIterTag = seqan::Rooted_; seqan::Parallel = seqan::Tag]’ /<>/apps/yara/mapper_classifier.h:114:12: required from ‘void _classifyReadsImpl(ReadsClassifier&, Strata) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; Strata = seqan::Tag]’ /<>/apps/yara/mapper_classifier.h:76:27: required from ‘ReadsClassifier::ReadsClassifier(ReadsClassifier::TReadsContext&, ReadsClassifier::THits&, const TSeeds&, const Options&) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; ReadsClassifier::TReadsContext = ReadsContext, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; ReadsClassifier::THits = seqan::String >, seqan::Alloc<> >; ReadsClassifier::TSeeds = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >, seqan::Segment, seqan::Alloc<> >, seqan::Owner > > > >]’ /<>/apps/yara/mapper.h:656:17: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_position.h:216:27: required from ‘void seqan::setCargo(seqan::ModifiedString >&, typename seqan::Parameter_::Type) [with THost = seqan::String >, seqan::Alloc<> >; TPositions = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /<>/include/seqan/modifier/modifier_position.h:357:13: required from ‘typename seqan::Infix > >::Type seqan::infix(seqan::ModifiedString >&, TPosBegin, TPosEnd) [with THost = seqan::String >, seqan::Alloc<> >; TPositions = seqan::String >; TPosBegin = long unsigned int; TPosEnd = long unsigned int; typename seqan::Infix > >::Type = seqan::ModifiedString >, seqan::Alloc<> >, seqan::ModPos >, seqan::InfixSegment> > >]’ /<>/include/seqan/sequence/segment_infix.h:649:17: required from ‘typename seqan::Infix::Type seqan::infixWithLength(T&&, TPosBegin, TSize) [with T = seqan::ModifiedString >, seqan::Alloc<> >, seqan::ModPos > > >; TPosBegin = long unsigned int; TSize = long unsigned int; typename seqan::Infix::Type = seqan::ModifiedString >, seqan::Alloc<> >, seqan::ModPos >, seqan::InfixSegment> > >]’ /<>/include/seqan/sequence/string_set_segment.h:489:27: required from ‘typename seqan::InfixOnValue::Type seqan::value(const seqan::StringSet >&, TPos) [with THost = seqan::ModifiedString >, seqan::Alloc<> >, seqan::ModPos > > >; TSpec = seqan::ModifiedString >, seqan::Alloc<> >, seqan::ModPos > > >; TPos = long unsigned int; typename seqan::InfixOnValue::Type = const seqan::ModifiedString >, seqan::Alloc<> >, seqan::ModPos >, seqan::InfixSegment> > >]’ /<>/include/seqan/basic/iterator_position.h:215:17: required from ‘typename seqan::Reference > > >::Type seqan::value(const seqan::Iter > >&) [with TContainer = const seqan::StringSet >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::Segment >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::InfixSegment> >; typename seqan::Reference > > >::Type = const seqan::ModifiedString >, seqan::Alloc<> >, seqan::ModPos >, seqan::InfixSegment> > >]’ /<>/apps/yara/mapper.h:885:53: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.h:1397:14: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:90: /<>/apps/yara/mapper_writer.h: In instantiation of ‘void setQual(seqan::BamAlignmentRecord&, const TString&) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/apps/yara/mapper_writer.h:455:12: required from ‘void _fillReadSeqQual(MatchesWriter&, TReadSeqId) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadSeqId = long unsigned int]’ /<>/apps/yara/mapper_writer.h:305:21: required from ‘void _writeMappedRead(MatchesWriter&, TReadId, const TMatch&, SingleEnd) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadId = long unsigned int; TMatch = Match >; SingleEnd = seqan::Tag]’ /<>/apps/yara/mapper_writer.h:236:25: required from ‘void _writeMatchesImpl(MatchesWriter&, const TMatchIt&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TMatchIt = seqan::Iter >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::ModPos > > >, seqan::CountingIteratorImpl_ > >]’ /<>/apps/yara/mapper_writer.h:102:26: required from ‘void MatchesWriter::operator()(const TIterator&) [with TIterator = seqan::Iter >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::ModPos > > >, seqan::CountingIteratorImpl_ > >; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /<>/include/seqan/parallel/parallel_algorithms.h:248:14: required from ‘void seqan::iterate(TContainer&, TFunctor, const seqan::Tag&, seqan::Parallel) [with TContainer = const seqan::ModifiedString >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::ModPos > > >; TFunctor = MatchesWriter, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >; TIterTag = seqan::Standard_; seqan::Parallel = seqan::Tag]’ /<>/apps/yara/mapper_writer.h:96:16: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/mapper_writer.h:164:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 164 | TQualities qual(string); | ^~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:81: /<>/apps/yara/find_extender.h: In instantiation of ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’: /<>/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /<>/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /<>/include/seqan/parallel/parallel_algorithms.h:248:14: required from ‘void seqan::iterate(TContainer&, TFunctor, const seqan::Tag&, seqan::Parallel) [with TContainer = const seqan::String >, seqan::Alloc<> >; TFunctor = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >; TIterTag = seqan::Standard_; seqan::Parallel = seqan::Tag]’ /<>/apps/yara/mapper_extender.h:134:12: required from ‘void _extendHitsImpl(HitsExtender&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper_extender.h:106:24: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/find_extender.h:220:25: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 220 | TNeedleInfixRev needleInfixRev(needleInfix); | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:81: /<>/apps/yara/find_extender.h:221:27: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 221 | THaystackInfixRev haystackInfixRev(haystackInfix); | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:81: /<>/apps/yara/find_extender.h:241:21: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 241 | TNeedleInfixRev needleInfixRev(needleInfix); | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:81: /<>/apps/yara/find_extender.h:242:23: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 242 | THaystackInfixRev haystackInfixRev(haystackInfix); | ^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/apps/yara/mapper.cpp:81: /<>/apps/yara/find_extender.h: In instantiation of ‘bool _extendRight(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’: /<>/apps/yara/find_extender.h:429:26: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /<>/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /<>/include/seqan/parallel/parallel_algorithms.h:248:14: required from ‘void seqan::iterate(TContainer&, TFunctor, const seqan::Tag&, seqan::Parallel) [with TContainer = const seqan::String >, seqan::Alloc<> >; TFunctor = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >; TIterTag = seqan::Standard_; seqan::Parallel = seqan::Tag]’ /<>/apps/yara/mapper_extender.h:134:12: required from ‘void _extendHitsImpl(HitsExtender&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper_extender.h:106:24: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/apps/yara/find_extender.h:311:20: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 311 | THaystackInfix haystackPrefix(haystackInfix); | ^~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/apps/yara/mapper.cpp:81: /<>/apps/yara/find_extender.h:312:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 312 | TNeedleInfix needlePrefix(needleInfix); | ^~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]’ /<>/include/seqan/bam_io/write_sam.h:114:14: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.h:402:19: required from ‘void openReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1397:14: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /<>/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/yara/mapper_writer.h:164:16: required from ‘void setQual(seqan::BamAlignmentRecord&, const TString&) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/yara/mapper_writer.h:455:12: required from ‘void _fillReadSeqQual(MatchesWriter&, TReadSeqId) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadSeqId = long unsigned int]’ /<>/apps/yara/mapper_writer.h:305:21: required from ‘void _writeMappedRead(MatchesWriter&, TReadId, const TMatch&, SingleEnd) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadId = long unsigned int; TMatch = Match >; SingleEnd = seqan::Tag]’ /<>/apps/yara/mapper_writer.h:236:25: required from ‘void _writeMatchesImpl(MatchesWriter&, const TMatchIt&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TMatchIt = seqan::Iter >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::ModPos > > >, seqan::CountingIteratorImpl_ > >]’ /<>/apps/yara/mapper_writer.h:102:26: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/apps/yara/find_extender.h:220:25: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /<>/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /<>/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /<>/include/seqan/parallel/parallel_algorithms.h:248:14: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Packed > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’: /<>/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ /<>/apps/yara/find_extender.h:221:27: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /<>/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /<>/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /<>/include/seqan/parallel/parallel_algorithms.h:248:14: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag]’: /<>/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /<>/apps/yara/find_extender.h:243:17: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /<>/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /<>/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /<>/include/seqan/parallel/parallel_algorithms.h:248:14: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >]’ /<>/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = void]’ /<>/apps/yara/find_extender.h:317:18: required from ‘bool _extendRight(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /<>/apps/yara/find_extender.h:429:26: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /<>/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper_extender.h:112:23: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /<>/apps/yara/find_extender.h:243:17: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /<>/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /<>/apps/yara/mapper_extender.h:216:15: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ /<>/include/seqan/align/gaps_anchor.h:180:26: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/gaps_anchor.h:180:26: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:650:46: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘void seqan::compare_(seqan::Lexical&, TLeft&, TRight&) [with TSpec = long unsigned int; TLeft = const seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = const seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/sequence/sequence_lexical.h:323:13: required from ‘void seqan::compare(seqan::Lexical&, const TLeft&, const TRight&) [with TSpec = long unsigned int; TLeft = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/sequence/sequence_lexical.h:170:16: required from ‘seqan::Lexical::Lexical(const TLeft&, const TRight&) [with TLeft = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = long unsigned int]’ /<>/include/seqan/sequence/sequence_lexical.h:750:38: required from ‘typename seqan::Size::Type seqan::lcpLength(const TLeft&, const TRight&) [with TLeft = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; typename seqan::Size::Type = long unsigned int]’ /<>/apps/yara/find_extender.h:222:24: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /<>/apps/yara/find_extender.h:413:25: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:61, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >]’: /<>/include/seqan/basic/iterator_interface.h:430:24: required from ‘void seqan::goEnd(TIterator&) [with TIterator = seqan::ModifiedIterator, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/find/find_base.h:737:10: required from ‘void seqan::goEnd(seqan::Finder&) [with THaystack = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1537:18: required from ‘bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFinderCSP = seqan::NMatchesNone_; TPatternCSP = seqan::NMatchesNone_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::AlignTextBanded; TFindBeginPatternSpec = void]’ /<>/apps/yara/find_extender.h:246:16: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /<>/apps/yara/find_extender.h:413:25: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:62, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/find.h:55, from /<>/include/seqan/index.h:46, from /<>/apps/yara/mapper.cpp:59: /<>/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’: /<>/include/seqan/find/find_myers_ukkonen.h:989:66: required from ‘bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Packed > >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindPrefix; TFinderCSP = seqan::NMatchesNone_; TPatternCSP = seqan::NMatchesNone_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1181:44: required from ‘bool seqan::_stateInit(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Packed > >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindPrefix; TFinderCSP = seqan::NMatchesNone_; TPatternCSP = seqan::NMatchesNone_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1535:24: required from ‘bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Packed > >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindPrefix; TFinderCSP = seqan::NMatchesNone_; TPatternCSP = seqan::NMatchesNone_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Packed > >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AlignTextBanded; TFindBeginPatternSpec = void]’ /<>/apps/yara/find_extender.h:320:16: required from ‘bool _extendRight(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /<>/apps/yara/find_extender.h:429:26: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:993:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:994:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:631:45: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Packed > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed > >, seqan::Packed > >, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:509:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/apps/yara/find_verifier.h:112:39: required from ‘void verify(Verifier >&, const TNeedle&, THaystackPos, THaystackPos, TErrors, TErrors, TDelegate&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TDelegate = AnchorsVerifier, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >]’ /<>/apps/yara/mapper_verifier.h:193:11: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:510:37: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/apps/yara/find_verifier.h:112:39: required from ‘void verify(Verifier >&, const TNeedle&, THaystackPos, THaystackPos, TErrors, TErrors, TDelegate&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TDelegate = AnchorsVerifier, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >]’ /<>/apps/yara/mapper_verifier.h:193:11: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/sequence/sequence_lexical.h:287:63: required from ‘void seqan::compare_(seqan::Lexical&, TLeft&, TRight&) [with TSpec = long unsigned int; TLeft = const seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = const seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/sequence/sequence_lexical.h:323:13: required from ‘void seqan::compare(seqan::Lexical&, const TLeft&, const TRight&) [with TSpec = long unsigned int; TLeft = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]’ /<>/include/seqan/sequence/sequence_lexical.h:170:16: required from ‘seqan::Lexical::Lexical(const TLeft&, const TRight&) [with TLeft = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = long unsigned int]’ /<>/include/seqan/sequence/sequence_lexical.h:750:38: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/modifier/modifier_reverse.h:503:103: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/find/find_myers_ukkonen.h:994:21: required from ‘bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFinderCSP = seqan::NMatchesNone_; TPatternCSP = seqan::NMatchesNone_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1181:44: required from ‘bool seqan::_stateInit(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFinderCSP = seqan::NMatchesNone_; TPatternCSP = seqan::NMatchesNone_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1535:24: required from ‘bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFinderCSP = seqan::NMatchesNone_; TPatternCSP = seqan::NMatchesNone_; TFindBeginPatternSpec = void]’ /<>/include/seqan/find/find_myers_ukkonen.h:1646:16: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:382:27: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::SimpleType; TSeqVValue = seqan::SimpleType; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/align/dp_algorithm_impl.h:453:18: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::SimpleType; TSeqVValue = seqan::SimpleType; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/align/dp_algorithm_impl.h:515:18: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/apps/yara/find_verifier.h:112:39: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /<>/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /<>/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /<>/apps/yara/mapper.cpp:422:44: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/mapper.cpp:58: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/mapper.cpp:57: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ [ 5%] Linking CXX executable ../../bin/stellar cd /<>/obj-x86_64-linux-gnu/apps/stellar && /usr/bin/cmake -E cmake_link_script CMakeFiles/stellar.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/stellar.dir/stellar.cpp.o -o ../../bin/stellar -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target stellar make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/apps/yara /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/apps/yara /<>/obj-x86_64-linux-gnu/apps/yara/CMakeFiles/yara_indexer.dir/DependInfo.cmake --color= Scanning dependencies of target yara_indexer make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object apps/yara/CMakeFiles/yara_indexer.dir/indexer.cpp.o cd /<>/obj-x86_64-linux-gnu/apps/yara && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.9.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DYARA_LARGE_CONTIGS=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/yara_indexer.dir/indexer.cpp.o -c /<>/apps/yara/indexer.cpp In file included from /<>/include/seqan/index.h:194, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/index/index_pizzachili.h: In function ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’: /<>/include/seqan/index/index_pizzachili.h:320:30: warning: ‘bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)’ is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /<>/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /<>/apps/yara/store_seqs.h:209:20: required from ‘void trimSeqNames(SeqStore&) [with TSpec = void; TConfig = YaraContigsConfig<>]’ /<>/apps/yara/indexer.cpp:201:21: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:357:24: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/apps/yara/store_seqs.h:209:34: required from ‘void trimSeqNames(SeqStore&) [with TSpec = void; TConfig = YaraContigsConfig<>]’ /<>/apps/yara/indexer.cpp:201:21: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:357:24: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:357:24: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]’: /<>/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /<>/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]’ /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]’: /<>/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:357:24: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /<>/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]’ /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]’ /<>/apps/yara/store_seqs.h:209:34: required from ‘void trimSeqNames(SeqStore&) [with TSpec = void; TConfig = YaraContigsConfig<>]’ /<>/apps/yara/indexer.cpp:201:21: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:357:24: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:357:24: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:357:24: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/stream.h:75, from /<>/include/seqan/score.h:43, from /<>/include/seqan/find.h:45, from /<>/include/seqan/index.h:46, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]’: /<>/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]’ /<>/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]’ /<>/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]’ /<>/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /<>/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:357:24: required from here /<>/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/apps/yara/indexer.cpp:49: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/modifier.h:75, from /<>/include/seqan/file.h:59, from /<>/include/seqan/pipe.h:41, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:186:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:186:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:186:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:186:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:186:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:186:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > > > >; TAlgSpec = seqan::Skew7]’ /<>/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /<>/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /<>/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:312:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:56, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew7.h:376:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /<>/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TContigsLen = long unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:321:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:342:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /<>/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew3.h:218:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /<>/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /<>/include/seqan/index/index_skew3.h:218:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/pipe_merger7.h:320:13: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]’: /<>/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /<>/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /<>/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /<>/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /<>/include/seqan/index/index_skew3.h:329:13: [ skipping 16 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /<>/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /<>/apps/yara/indexer.cpp:360:22: required from here /<>/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /<>/include/seqan/pipe.h:74, from /<>/include/seqan/index.h:42, from /<>/apps/yara/indexer.cpp:50: /<>/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_aggregate.h:58, from /<>/include/seqan/basic.h:98, from /<>/apps/yara/indexer.cpp:48: /<>/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 5%] Linking CXX executable ../../bin/yara_indexer cd /<>/obj-x86_64-linux-gnu/apps/yara && /usr/bin/cmake -E cmake_link_script CMakeFiles/yara_indexer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/yara_indexer.dir/indexer.cpp.o -o ../../bin/yara_indexer -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target yara_indexer make -f tests/align/CMakeFiles/test_align.dir/build.make tests/align/CMakeFiles/test_align.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align.dir/DependInfo.cmake --color= Scanning dependencies of target test_align make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align.dir/build.make tests/align/CMakeFiles/test_align.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object tests/align/CMakeFiles/test_align.dir/test_align.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align.dir/test_align.cpp.o -c /<>/tests/align/test_align.cpp In file included from /<>/include/seqan/align.h:83, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_base.h: In instantiation of ‘seqan::Iter > seqan::operator++(seqan::Iter >&, int) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TSpec = seqan::AnchorGaps<>]’: /<>/tests/align/test_align_gaps_iterator.h:183:11: required from ‘void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]’ /<>/tests/align/test_align_gaps_iterator.h:1157:34: required from ‘void SEQAN_TEST_test_align_gaps_iterator_anchor_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:156:5: required from here /<>/include/seqan/align/gaps_iterator_base.h:205:39: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 205 | Iter > ret = it; | ^~~ In file included from /<>/include/seqan/align.h:90, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:83, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_base.h:207:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 207 | return ret; | ^~~ In file included from /<>/include/seqan/align.h:90, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:83, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_base.h: In instantiation of ‘seqan::Iter > seqan::operator--(seqan::Iter >&, int) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TSpec = seqan::AnchorGaps<>]’: /<>/tests/align/test_align_gaps_iterator.h:219:11: required from ‘void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]’ /<>/tests/align/test_align_gaps_iterator.h:1157:34: required from ‘void SEQAN_TEST_test_align_gaps_iterator_anchor_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:156:5: required from here /<>/include/seqan/align/gaps_iterator_base.h:226:39: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 226 | Iter > ret = it; | ^~~ In file included from /<>/include/seqan/align.h:90, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:83, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_base.h:228:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 228 | return ret; | ^~~ In file included from /<>/include/seqan/align.h:90, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; TDifference = int]’: /<>/tests/align/test_align_gaps_iterator.h:345:5: required from ‘void testAlignGapsIteratorPointerArithmetic(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]’ /<>/tests/align/test_align_gaps_iterator.h:1171:43: required from ‘void SEQAN_TEST_test_align_gaps_iterator_anchor_pointer_arithmetic() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:158:5: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator-(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; TDifference = int]’: /<>/tests/align/test_align_gaps_iterator.h:346:5: required from ‘void testAlignGapsIteratorPointerArithmetic(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]’ /<>/tests/align/test_align_gaps_iterator.h:1171:43: required from ‘void SEQAN_TEST_test_align_gaps_iterator_anchor_pointer_arithmetic() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:158:5: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:760:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 760 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:762:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 762 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’: /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:627:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’: /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:627:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h: In instantiation of ‘TScoreValue seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const Hirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; seqan::Hirschberg = seqan::Tag]’: /<>/include/seqan/align/global_alignment_specialized.h:72:28: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score >&, const Hirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; seqan::Hirschberg = seqan::Tag]’ /<>/tests/align/test_align_global_alignment_specialized.h:167:36: required from ‘void SEQAN_TEST_test_align_global_alignment_hirschberg_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:595:5: required from here /<>/include/seqan/align/global_alignment_hirschberg_impl.h:468:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 468 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:487:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 487 | finger2 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:489:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 489 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:518:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 518 | finger1 = begin(matrix_); | ~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:543:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 543 | it_ = finger1; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of ‘int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’: /<>/include/seqan/align/global_alignment_specialized.h:95:28: required from ‘int seqan::globalAlignment(seqan::Align&, const MyersHirschberg&) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’ /<>/tests/align/test_align_global_alignment_specialized.h:205:36: required from ‘void SEQAN_TEST_test_align_global_alignment_myers_hirschberg_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:599:5: required from here /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 348 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 368 | finger2 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 370 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 398 | finger1 = begin(matrix_); | ~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 423 | it_ = finger1; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of ‘int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’: /<>/include/seqan/align/global_alignment_specialized.h:104:28: required from ‘int seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’ /<>/tests/align/test_align_global_alignment_specialized.h:231:36: required from ‘void SEQAN_TEST_test_align_global_alignment_myers_hirschberg_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:600:5: required from here /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 348 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 368 | finger2 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 370 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 398 | finger1 = begin(matrix_); | ~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 423 | it_ = finger1; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of ‘int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = const seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = const seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’: /<>/include/seqan/align/global_alignment_specialized.h:167:28: required from ‘int seqan::globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersHirschberg&) [with TAlphabetH = seqan::SimpleType; TSpecH = seqan::Alloc<>; TAlphabetV = seqan::SimpleType; TSpecV = seqan::Alloc<>; seqan::MyersHirschberg = seqan::Tag]’ /<>/tests/align/test_align_global_alignment_specialized.h:311:31: required from ‘void SEQAN_TEST_test_align_global_alignment_score_myers_hirschberg() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:606:5: required from here /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 348 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 368 | finger2 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 370 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 398 | finger1 = begin(matrix_); | ~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 423 | it_ = finger1; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >]’: /<>/include/seqan/align/gaps_anchor.h:226:43: required from ‘typename seqan::Reference > >::Type seqan::Gaps >::operator[](seqan::Gaps >::TPosition_) [with TSource = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String >; typename seqan::Reference > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >; seqan::Gaps >::TPosition_ = long int]’ /<>/tests/align/test_align_gaps.h:205:9: required from ‘void testAlignGapsGapOperationsGapCenter(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]’ /<>/tests/align/test_align_gaps.h:1633:40: required from ‘void SEQAN_TEST_test_align_gaps_anchor_gaps_gap_operations_gaps_center() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:104:5: required from here /<>/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 94 | : data_iterator(_other.data_iterator) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >]’: /<>/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TSpec = seqan::GapsIterator >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >]’ /<>/tests/align/test_align_gaps.h:835:5: required from ‘void testAlignGapsIteratorInterfaceBegin(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]’ /<>/tests/align/test_align_gaps.h:1682:40: required from ‘void SEQAN_TEST_test_align_gaps_anchor_gaps_iterator_interface_begin() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:111:5: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ In file included from /<>/include/seqan/basic/basic_iterator.h:56, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_interface.h: In instantiation of ‘void seqan::goEnd(TIterator&, TContainer&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >; TContainer = seqan::Gaps, seqan::Alloc<> > >]’: /<>/include/seqan/basic/iterator_interface.h:430:10: required from ‘void seqan::goEnd(TIterator&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >]’ /<>/tests/align/test_align_gaps_iterator.h:274:14: required from ‘void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::Tag]’ /<>/tests/align/test_align_gaps_iterator.h:1062:34: required from ‘void SEQAN_TEST_test_align_gaps_iterator_array_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:142:5: required from here /<>/include/seqan/basic/iterator_interface.h:415:8: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 415 | it = end(container); | ~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> > >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:56, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_interface.h: In instantiation of ‘void seqan::goBegin(TIterator&, TContainer&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >; TContainer = seqan::Gaps, seqan::Alloc<> > >]’: /<>/include/seqan/basic/iterator_interface.h:403:12: required from ‘void seqan::goBegin(TIterator&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >]’ /<>/tests/align/test_align_gaps_iterator.h:281:16: required from ‘void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::Tag]’ /<>/tests/align/test_align_gaps_iterator.h:1062:34: required from ‘void SEQAN_TEST_test_align_gaps_iterator_array_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:142:5: required from here /<>/include/seqan/basic/iterator_interface.h:387:8: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 387 | it = begin(container); | ~~~^~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> > >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h: In instantiation of ‘bool _validateAlignment(const TAlignment&, const seqan::AlignConfig&, const TScore&, const seqan::Score >&) [with TAlignment = seqan::Align, seqan::Alloc<> > >; bool FreeTop = false; bool FreeLeft = false; bool FreeRight = false; bool FreeBottom = false; TACSpec = seqan::Tag; TScore = int]’: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:194:9: required from ‘void testDynamicGapInterfaces(TAlign&, const TAlgorithm&, const TAlignConfig&, int, int) [with TAlign = seqan::Align, seqan::Alloc<> > >; TAlgorithm = seqan::Tag; TAlignConfig = seqan::AlignConfig<>]’ /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:224:33: required from ‘void testDynamicGapInterfaces(const TAlgorithm&, const TAlignConfig&, int, int) [with TAlgorithm = seqan::Tag; TAlignConfig = seqan::AlignConfig<>]’ /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:271:29: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_dynamic_cost() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:494:5: required from here /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:109:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 109 | itH = begin(row(align, 0), Standard()); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:125:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 125 | itV = begin(row(align, 1), Standard()); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:141:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 141 | itH = end(row(align, 0), Standard()) - 1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:157:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 157 | itV = end(row(align, 1), Standard()) - 1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h: In instantiation of ‘bool _validateAlignment(const TAlignment&, const seqan::AlignConfig&, const TScore&, const seqan::Score >&) [with TAlignment = seqan::Align, seqan::Alloc<> > >; bool FreeTop = false; bool FreeLeft = true; bool FreeRight = true; bool FreeBottom = false; TACSpec = seqan::Tag; TScore = int]’: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:194:9: required from ‘void testDynamicGapInterfaces(TAlign&, const TAlgorithm&, const TAlignConfig&, int, int) [with TAlign = seqan::Align, seqan::Alloc<> > >; TAlgorithm = seqan::Tag; TAlignConfig = seqan::AlignConfig]’ /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:224:33: required from ‘void testDynamicGapInterfaces(const TAlgorithm&, const TAlignConfig&, int, int) [with TAlgorithm = seqan::Tag; TAlignConfig = seqan::AlignConfig]’ /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:272:29: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_dynamic_cost() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:494:5: required from here /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:109:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 109 | itH = begin(row(align, 0), Standard()); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:125:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 125 | itV = begin(row(align, 1), Standard()); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:141:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 141 | itH = end(row(align, 0), Standard()) - 1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:157:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 157 | itV = end(row(align, 1), Standard()) - 1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h: In instantiation of ‘bool _validateAlignment(const TAlignment&, const seqan::AlignConfig&, const TScore&, const seqan::Score >&) [with TAlignment = seqan::Align, seqan::Alloc<> > >; bool FreeTop = true; bool FreeLeft = false; bool FreeRight = false; bool FreeBottom = true; TACSpec = seqan::Tag; TScore = int]’: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:194:9: required from ‘void testDynamicGapInterfaces(TAlign&, const TAlgorithm&, const TAlignConfig&, int, int) [with TAlign = seqan::Align, seqan::Alloc<> > >; TAlgorithm = seqan::Tag; TAlignConfig = seqan::AlignConfig]’ /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:224:33: required from ‘void testDynamicGapInterfaces(const TAlgorithm&, const TAlignConfig&, int, int) [with TAlgorithm = seqan::Tag; TAlignConfig = seqan::AlignConfig]’ /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:273:29: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_dynamic_cost() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:494:5: required from here /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:109:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 109 | itH = begin(row(align, 0), Standard()); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:125:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 125 | itV = begin(row(align, 1), Standard()); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:141:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 141 | itH = end(row(align, 0), Standard()) - 1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:157:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 157 | itV = end(row(align, 1), Standard()) - 1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h: In instantiation of ‘bool _validateAlignment(const TAlignment&, const seqan::AlignConfig&, const TScore&, const seqan::Score >&) [with TAlignment = seqan::Align, seqan::Alloc<> > >; bool FreeTop = true; bool FreeLeft = true; bool FreeRight = true; bool FreeBottom = true; TACSpec = seqan::Tag; TScore = int]’: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:194:9: required from ‘void testDynamicGapInterfaces(TAlign&, const TAlgorithm&, const TAlignConfig&, int, int) [with TAlign = seqan::Align, seqan::Alloc<> > >; TAlgorithm = seqan::Tag; TAlignConfig = seqan::AlignConfig]’ /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:224:33: required from ‘void testDynamicGapInterfaces(const TAlgorithm&, const TAlignConfig&, int, int) [with TAlgorithm = seqan::Tag; TAlignConfig = seqan::AlignConfig]’ /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:274:29: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_dynamic_cost() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:494:5: required from here /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:109:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 109 | itH = begin(row(align, 0), Standard()); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:125:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 125 | itV = begin(row(align, 1), Standard()); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:141:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 141 | itH = end(row(align, 0), Standard()) - 1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/tests/align/test_align.cpp:60: /<>/tests/align/test_alignment_algorithms_dynamic_gap.h:157:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 157 | itV = end(row(align, 1), Standard()) - 1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:86, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_array.h:91:5: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]’ 91 | Iter(Iter const & other) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:395:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:500:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:395:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:500:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:235:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 235 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:253:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 253 | finger2 = col_; //points to last column | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:255:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 255 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::_smithWatermanTrace(seqan::Gaps&, seqan::Gaps&, typename seqan::LocalAlignmentFinder::TBoolMatrix&, seqan::Iter, seqan::CountingIteratorImpl_ > >, const seqan::Score&) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; unsigned int DIMENSION = 0; typename seqan::Iterator, const seqan::Tag >::Type = seqan::Iter, seqan::CountingIteratorImpl_ > >; typename seqan::LocalAlignmentFinder::TBoolMatrix = seqan::String]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:37: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:595:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 595 | it_ = source_; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘void seqan::_smithWatermanDeclump(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const seqan::Score&) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:736:26: required from ‘TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:445:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 445 | finger1 = end_col; //points to last column | ~~~~~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:447:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 447 | finger0 = end_col; | ~~~~~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:627:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:235:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 235 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:253:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 253 | finger2 = col_; //points to last column | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:255:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 255 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::_smithWatermanTrace(seqan::Gaps&, seqan::Gaps&, typename seqan::LocalAlignmentFinder::TBoolMatrix&, seqan::Iter, seqan::CountingIteratorImpl_ > >, const seqan::Score&) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; unsigned int DIMENSION = 0; typename seqan::Iterator, const seqan::Tag >::Type = seqan::Iter, seqan::CountingIteratorImpl_ > >; typename seqan::LocalAlignmentFinder::TBoolMatrix = seqan::String]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:37: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:627:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:595:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 595 | it_ = source_; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘void seqan::_smithWatermanDeclump(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const seqan::Score&) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:736:26: required from ‘TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:627:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:445:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 445 | finger1 = end_col; //points to last column | ~~~~~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:447:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 447 | finger0 = end_col; | ~~~~~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:190, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScore = seqan::Score >; TDiagonal = int]’: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScore = seqan::Score >; TDiagonal = int; seqan::BandedWatermanEggert = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local_banded.h:417:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_banded_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:575:5: required from here /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:190, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScore = seqan::Score, seqan::Blosum62_> >; TDiagonal = int]’: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScore = seqan::Score, seqan::Blosum62_> >; TDiagonal = int; seqan::BandedWatermanEggert = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local_banded.h:521:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_banded_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:575:5: required from here /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h: In instantiation of ‘TScoreValue seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const Hirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; seqan::Hirschberg = seqan::Tag]’: /<>/include/seqan/align/global_alignment_specialized.h:72:28: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score >&, const Hirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; seqan::Hirschberg = seqan::Tag]’ /<>/include/seqan/align/global_alignment_specialized.h:83:27: required from ‘TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score >&, const Hirschberg&) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TScoreValue = int; seqan::Hirschberg = seqan::Tag]’ /<>/tests/align/test_align_global_alignment_specialized.h:139:36: required from ‘void SEQAN_TEST_test_align_global_alignment_hirschberg_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:594:5: required from here /<>/include/seqan/align/global_alignment_hirschberg_impl.h:468:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 468 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:487:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 487 | finger2 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:489:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 489 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:518:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 518 | finger1 = begin(matrix_); | ~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:543:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 543 | it_ = finger1; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of ‘int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:199:32: required from ‘int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’ /<>/include/seqan/align/global_alignment_specialized.h:104:28: required from ‘int seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’ /<>/tests/align/test_align_global_alignment_specialized.h:231:36: required from ‘void SEQAN_TEST_test_align_global_alignment_myers_hirschberg_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:600:5: required from here /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 348 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 368 | finger2 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 370 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 398 | finger1 = begin(matrix_); | ~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 423 | it_ = finger1; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h: In instantiation of ‘TScoreValue seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const Hirschberg&) [with TSequenceH = const seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = const seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; seqan::Hirschberg = seqan::Tag]’: /<>/include/seqan/align/global_alignment_specialized.h:72:28: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score >&, const Hirschberg&) [with TSequenceH = const seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = const seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; seqan::Hirschberg = seqan::Tag]’ /<>/include/seqan/align/global_alignment_specialized.h:142:27: required from ‘TScoreValue seqan::globalAlignmentScore(const seqan::String&, const seqan::String&, const seqan::Score >&, const Hirschberg&) [with TAlphabetH = seqan::SimpleType; TSpecH = seqan::Alloc<>; TAlphabetV = seqan::SimpleType; TSpecV = seqan::Alloc<>; TScoreValue = int; seqan::Hirschberg = seqan::Tag]’ /<>/tests/align/test_align_global_alignment_specialized.h:270:31: required from ‘void SEQAN_TEST_test_align_global_alignment_score_hirschberg() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:604:5: required from here /<>/include/seqan/align/global_alignment_hirschberg_impl.h:468:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 468 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:487:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 487 | finger2 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:489:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 489 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:518:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 518 | finger1 = begin(matrix_); | ~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:543:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 543 | it_ = finger1; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of ‘int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = const seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = const seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:199:32: required from ‘int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = const seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = const seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’ /<>/include/seqan/align/global_alignment_specialized.h:167:28: required from ‘int seqan::globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersHirschberg&) [with TAlphabetH = seqan::SimpleType; TSpecH = seqan::Alloc<>; TAlphabetV = seqan::SimpleType; TSpecV = seqan::Alloc<>; seqan::MyersHirschberg = seqan::Tag]’ /<>/tests/align/test_align_global_alignment_specialized.h:311:31: required from ‘void SEQAN_TEST_test_align_global_alignment_score_myers_hirschberg() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:606:5: required from here /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 348 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 368 | finger2 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 370 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 398 | finger1 = begin(matrix_); | ~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 423 | it_ = finger1; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of ‘int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = const seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = const seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]’: /<>/include/seqan/align/global_alignment_specialized.h:167:28: required from ‘int seqan::globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersHirschberg&) [with TAlphabetH = seqan::SimpleType; TSpecH = seqan::Alloc<>; TAlphabetV = seqan::SimpleType; TSpecV = seqan::Alloc<>; seqan::MyersHirschberg = seqan::Tag]’ /<>/include/seqan/align/global_alignment_specialized.h:175:32: required from ‘int seqan::globalAlignmentScore(const seqan::StringSet&, const MyersHirschberg&) [with TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner<>; seqan::MyersHirschberg = seqan::Tag]’ /<>/tests/align/test_align_global_alignment_specialized.h:314:31: required from ‘void SEQAN_TEST_test_align_global_alignment_score_myers_hirschberg() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:606:5: required from here /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 348 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 368 | finger2 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 370 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 398 | finger1 = begin(matrix_); | ~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:183, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 423 | it_ = finger1; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:90, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; TDifference = long int]’: /<>/include/seqan/align/gaps_base.h:294:86: required from ‘typename seqan::Reference >::Type seqan::value(seqan::Gaps&, TPosition) [with TSequence = seqan::String, seqan::Alloc<> >; TSpec = seqan::AnchorGaps<>; TPosition = long int; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >]’ /<>/include/seqan/align/gaps_anchor.h:226:21: required from ‘typename seqan::Reference > >::Type seqan::Gaps >::operator[](seqan::Gaps >::TPosition_) [with TSource = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String >; typename seqan::Reference > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >; seqan::Gaps >::TPosition_ = long int]’ /<>/tests/align/test_align_gaps.h:205:9: required from ‘void testAlignGapsGapOperationsGapCenter(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]’ /<>/tests/align/test_align_gaps.h:1633:40: required from ‘void SEQAN_TEST_test_align_gaps_anchor_gaps_gap_operations_gaps_center() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:104:5: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:87, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >]’: /<>/include/seqan/align/gaps_base.h:294:57: required from ‘typename seqan::Reference >::Type seqan::value(seqan::Gaps&, TPosition) [with TSequence = seqan::String, seqan::Alloc<> >; TSpec = seqan::AnchorGaps<>; TPosition = long int; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >]’ /<>/include/seqan/align/gaps_anchor.h:226:21: required from ‘typename seqan::Reference > >::Type seqan::Gaps >::operator[](seqan::Gaps >::TPosition_) [with TSource = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String >; typename seqan::Reference > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >; seqan::Gaps >::TPosition_ = long int]’ /<>/tests/align/test_align_gaps.h:205:9: required from ‘void testAlignGapsGapOperationsGapCenter(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]’ /<>/tests/align/test_align_gaps.h:1633:40: required from ‘void SEQAN_TEST_test_align_gaps_anchor_gaps_gap_operations_gaps_center() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:104:5: required from here /<>/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^ In file included from /<>/include/seqan/align.h:90, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; TDifference = int]’: /<>/include/seqan/sequence/sequence_interface.h:689:35: required from ‘typename seqan::Iterator >::Type seqan::iter(const T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TPos = int; TTag = seqan::Standard_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >]’ /<>/include/seqan/align/gaps_base.h:475:28: required from ‘bool seqan::isCharacter(const seqan::Gaps&, TPos) [with TSequence = seqan::String, seqan::Alloc<> >; TSpec = seqan::AnchorGaps<>; TPos = int]’ /<>/tests/align/test_align_gaps.h:214:9: required from ‘void testAlignGapsGapOperationsGapCenter(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]’ /<>/tests/align/test_align_gaps.h:1633:40: required from ‘void SEQAN_TEST_test_align_gaps_anchor_gaps_gap_operations_gaps_center() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:104:5: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; TDifference = int]’: /<>/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps >, seqan::AnchorGaps<> >; TPos = int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::AnchorGaps<> >, seqan::GapsIterator > >]’ /<>/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps >, seqan::AnchorGaps<> >; TPos = int; typename seqan::Iterator::Type>::Type = seqan::Iter >, seqan::AnchorGaps<> >, seqan::GapsIterator > >]’ /<>/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::String >; TGapAnchors = seqan::String >; TPosition = int; TCount = int]’ /<>/tests/align/test_align_gaps.h:1795:15: required from ‘void SEQAN_TEST_test_align_gaps_anchor_gaps_clear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:127:5: required from here /<>/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /<>/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps<> >, seqan::GapsIterator > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:395:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:500:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:235:13: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 235 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:253:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 253 | finger2 = col_; //points to last column | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:255:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 255 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::_smithWatermanTrace(seqan::Gaps&, seqan::Gaps&, typename seqan::LocalAlignmentFinder::TBoolMatrix&, seqan::Iter, seqan::CountingIteratorImpl_ > >, const seqan::Score&) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; unsigned int DIMENSION = 0; typename seqan::Iterator, const seqan::Tag >::Type = seqan::Iter, seqan::CountingIteratorImpl_ > >; typename seqan::LocalAlignmentFinder::TBoolMatrix = seqan::String]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:37: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:395:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:500:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:595:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 595 | it_ = source_; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of ‘void seqan::_smithWatermanDeclump(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const seqan::Score&) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:736:26: required from ‘TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:395:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:500:5: required from here /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:445:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 445 | finger1 = end_col; //points to last column | ~~~~~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:189, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:447:17: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 447 | finger0 = end_col; | ~~~~~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:22: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:217:44: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:217:22: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:627:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:22: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:627:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/align.h:190, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScore = seqan::Score >; TDiagonal = int]’: /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScore = seqan::Score >; TDiagonal = int; seqan::BandedWatermanEggert = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local_banded.h:304:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_banded_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:574:5: required from here /<>/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h: In instantiation of ‘TScoreValue seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const Hirschberg&) [with TSequenceH = const seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = const seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; seqan::Hirschberg = seqan::Tag]’: /<>/include/seqan/align/global_alignment_specialized.h:72:28: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score >&, const Hirschberg&) [with TSequenceH = const seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = const seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; seqan::Hirschberg = seqan::Tag]’ /<>/include/seqan/align/global_alignment_specialized.h:142:27: required from ‘TScoreValue seqan::globalAlignmentScore(const seqan::String&, const seqan::String&, const seqan::Score >&, const Hirschberg&) [with TAlphabetH = seqan::SimpleType; TSpecH = seqan::Alloc<>; TAlphabetV = seqan::SimpleType; TSpecV = seqan::Alloc<>; TScoreValue = int; seqan::Hirschberg = seqan::Tag]’ /<>/include/seqan/align/global_alignment_specialized.h:152:32: required from ‘TScoreValue seqan::globalAlignmentScore(const seqan::StringSet&, const seqan::Score&, const Hirschberg&) [with TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner<>; TScoreValue = int; TScoreSpec = seqan::Tag; seqan::Hirschberg = seqan::Tag]’ /<>/tests/align/test_align_global_alignment_specialized.h:274:31: required from ‘void SEQAN_TEST_test_align_global_alignment_score_hirschberg() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:604:5: required from here /<>/include/seqan/align/global_alignment_hirschberg_impl.h:468:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 468 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:487:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 487 | finger2 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:489:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 489 | finger1 = col_; | ~~~~~~~~^~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:518:21: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 518 | finger1 = begin(matrix_); | ~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/align.h:177, from /<>/tests/align/test_align_stream.h:40, from /<>/tests/align/test_align.cpp:38: /<>/include/seqan/align/global_alignment_hirschberg_impl.h:543:25: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 543 | it_ = finger1; | ~~~~^~~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:74, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:525:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_unbanded.h:258:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global.h:2654:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:480:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:526:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_unbanded.h:258:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global.h:2654:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:480:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:509:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_unbanded.h:258:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global.h:2682:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:480:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /<>/include/seqan/sequence.h:97, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:37: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:504:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:216:33: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:217:37: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:217:44: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:504:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:218:33: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:515:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:37: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:627:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:627:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/sequence/sequence_interface.h:504:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:216:33: required from ‘TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from ‘TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]’ /<>/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from ‘bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_local.h:627:9: required from ‘void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:501:5: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global_banded.h:1979:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_banded_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:556:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global_banded.h:1979:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_banded_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:556:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global_banded.h:2007:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_banded_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:556:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:525:40: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_unbanded.h:258:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global.h:2654:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:480:5: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:526:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_unbanded.h:258:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global.h:2654:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:480:5: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:509:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_unbanded.h:258:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global.h:2682:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:480:5: required from here /<>/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:94, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]’: /<>/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]’ /<>/include/seqan/align/dp_algorithm_impl.h:510:37: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_unbanded.h:258:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global.h:2682:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:480:5: required from here /<>/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /<>/include/seqan/align/dp_algorithm_impl.h:993:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global_banded.h:2007:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_banded_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:556:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /<>/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long int]’: /<>/include/seqan/align/dp_algorithm_impl.h:994:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global_banded.h:2007:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_banded_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:556:5: required from here /<>/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_iterator.h:80, from /<>/include/seqan/basic.h:86, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Reference > >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’ /<>/include/seqan/align/gaps_array.h:427:10: required from ‘void seqan::assignSource(seqan::Gaps >&, const TSequence2&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequence2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /<>/tests/align/test_align_alignment_operations.h:69:21: required from ‘void SEQAN_TEST_test_align_integrate_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:613:5: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:96, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Reference > >::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&]’ /<>/include/seqan/align/gaps_array.h:269:34: required from ‘void seqan::_reinitArrayGaps(seqan::Gaps >&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ /<>/include/seqan/align/gaps_array.h:155:25: required from ‘seqan::Gaps >::Gaps(TSequence&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ /<>/tests/align/test_alignment_algorithms_global.h:2648:61: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:480:5: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:526:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_unbanded.h:258:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global.h:2654:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:480:5: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:98, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&]’ /<>/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Reference > >::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&]’ /<>/include/seqan/align/gaps_array.h:269:34: required from ‘void seqan::_reinitArrayGaps(seqan::Gaps >&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/include/seqan/align/gaps_array.h:155:25: required from ‘seqan::Gaps >::Gaps(TSequence&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/tests/align/test_alignment_algorithms_global.h:2678:61: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:480:5: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/sequence.h:97, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /<>/include/seqan/sequence.h:95, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’: /<>/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]’ /<>/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]’ /<>/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]’ /<>/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]’ /<>/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = false; bool LEFT = false; bool RIGHT = false; bool BOTTOM = false; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]’ /<>/tests/align/test_alignment_algorithms_global_banded.h:2007:36: required from ‘void SEQAN_TEST_test_alignment_algorithms_global_banded_different_container() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]’ /<>/tests/align/test_align.cpp:556:5: required from here /<>/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /<>/include/seqan/sequence.h:97, from /<>/include/seqan/file.h:58, from /<>/include/seqan/stream.h:62, from /<>/tests/align/test_align.cpp:36: /<>/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ [ 5%] Linking CXX executable ../../bin/test_align cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align.dir/test_align.cpp.o -o ../../bin/test_align -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target test_align make -f tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_global_variable_length make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/test_align_simd_global_variable_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_global_variable_length.dir/test_align_simd_global_variable_length.cpp.o -c /<>/tests/align/test_align_simd_global_variable_length.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_variable_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_variable_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_variable_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_variable_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ [ 5%] Linking CXX executable ../../bin/test_align_simd_global_variable_length cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_global_variable_length.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_global_variable_length.dir/test_align_simd_global_variable_length.cpp.o -o ../../bin/test_align_simd_global_variable_length -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target test_align_simd_global_variable_length make -f tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_local_equal_length make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/test_align_simd_local_equal_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_local_equal_length.dir/test_align_simd_local_equal_length.cpp.o -c /<>/tests/align/test_align_simd_local_equal_length.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_local_equal_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_local.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_local.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_local_equal_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_local_equal_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_local.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_local.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_local_equal_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ [ 5%] Linking CXX executable ../../bin/test_align_simd_local_equal_length cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_local_equal_length.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_local_equal_length.dir/test_align_simd_local_equal_length.cpp.o -o ../../bin/test_align_simd_local_equal_length -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target test_align_simd_local_equal_length make -f tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_global_equal_length make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/test_align_simd_global_equal_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_global_equal_length.dir/test_align_simd_global_equal_length.cpp.o -c /<>/tests/align/test_align_simd_global_equal_length.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_equal_length.cpp:36: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_equal_length.cpp:39: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_equal_length.cpp:36: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_equal_length.cpp:39: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ [ 5%] Linking CXX executable ../../bin/test_align_simd_global_equal_length cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_global_equal_length.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_global_equal_length.dir/test_align_simd_global_equal_length.cpp.o -o ../../bin/test_align_simd_global_equal_length -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target test_align_simd_global_equal_length make -f tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_local_variable_length make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/test_align_simd_local_variable_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_local_variable_length.dir/test_align_simd_local_variable_length.cpp.o -c /<>/tests/align/test_align_simd_local_variable_length.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_local_variable_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_local.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_local.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_local_variable_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_local_variable_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_local.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_local.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_local_variable_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ [ 5%] Linking CXX executable ../../bin/test_align_simd_local_variable_length cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_local_variable_length.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_local_variable_length.dir/test_align_simd_local_variable_length.cpp.o -o ../../bin/test_align_simd_local_variable_length -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 5%] Built target test_align_simd_local_variable_length make -f tests/align/CMakeFiles/test_align_simd_global_variable_length_sse4.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length_sse4.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length_sse4.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_global_variable_length_sse4 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_global_variable_length_sse4.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length_sse4.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 6%] Building CXX object tests/align/CMakeFiles/test_align_simd_global_variable_length_sse4.dir/test_align_simd_global_variable_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -msse4 -o CMakeFiles/test_align_simd_global_variable_length_sse4.dir/test_align_simd_global_variable_length.cpp.o -c /<>/tests/align/test_align_simd_global_variable_length.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_variable_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_variable_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_variable_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_variable_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ [ 7%] Linking CXX executable ../../bin/yara_mapper cd /<>/obj-x86_64-linux-gnu/apps/yara && /usr/bin/cmake -E cmake_link_script CMakeFiles/yara_mapper.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/yara_mapper.dir/mapper.cpp.o -o ../../bin/yara_mapper -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 7%] Built target yara_mapper make -f tests/align/CMakeFiles/test_align_simd_local_equal_length_sse4.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length_sse4.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length_sse4.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_local_equal_length_sse4 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_local_equal_length_sse4.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length_sse4.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 7%] Building CXX object tests/align/CMakeFiles/test_align_simd_local_equal_length_sse4.dir/test_align_simd_local_equal_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -msse4 -o CMakeFiles/test_align_simd_local_equal_length_sse4.dir/test_align_simd_local_equal_length.cpp.o -c /<>/tests/align/test_align_simd_local_equal_length.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_local_equal_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_local.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_local.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_local_equal_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_local_equal_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_local.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_local.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_local_equal_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ [ 7%] Linking CXX executable ../../bin/test_align_simd_local_equal_length_sse4 cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_local_equal_length_sse4.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_local_equal_length_sse4.dir/test_align_simd_local_equal_length.cpp.o -o ../../bin/test_align_simd_local_equal_length_sse4 -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 7%] Built target test_align_simd_local_equal_length_sse4 make -f tests/align/CMakeFiles/test_align_simd_local_equal_length_avx2.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length_avx2.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length_avx2.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_local_equal_length_avx2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_local_equal_length_avx2.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length_avx2.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 7%] Building CXX object tests/align/CMakeFiles/test_align_simd_local_equal_length_avx2.dir/test_align_simd_local_equal_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -mavx2 -o CMakeFiles/test_align_simd_local_equal_length_avx2.dir/test_align_simd_local_equal_length.cpp.o -c /<>/tests/align/test_align_simd_local_equal_length.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_local_equal_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_local.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_local.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_local_equal_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_local_equal_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_local.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_local.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_local_equal_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ [ 7%] Linking CXX executable ../../bin/test_align_simd_global_variable_length_sse4 cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_global_variable_length_sse4.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_global_variable_length_sse4.dir/test_align_simd_global_variable_length.cpp.o -o ../../bin/test_align_simd_global_variable_length_sse4 -lrt -lz -lbz2 [ 7%] Linking CXX executable ../../bin/test_align_simd_local_equal_length_avx2 cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_local_equal_length_avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_local_equal_length_avx2.dir/test_align_simd_local_equal_length.cpp.o -o ../../bin/test_align_simd_local_equal_length_avx2 -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 7%] Built target test_align_simd_global_variable_length_sse4 make -f tests/align/CMakeFiles/test_align_simd_global_equal_length_sse4.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length_sse4.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length_sse4.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_global_equal_length_sse4 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_global_equal_length_sse4.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length_sse4.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 7%] Building CXX object tests/align/CMakeFiles/test_align_simd_global_equal_length_sse4.dir/test_align_simd_global_equal_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -msse4 -o CMakeFiles/test_align_simd_global_equal_length_sse4.dir/test_align_simd_global_equal_length.cpp.o -c /<>/tests/align/test_align_simd_global_equal_length.cpp make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 7%] Built target test_align_simd_local_equal_length_avx2 make -f tests/align/CMakeFiles/test_align_simd_local_variable_length_sse4.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length_sse4.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length_sse4.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_local_variable_length_sse4 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_local_variable_length_sse4.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length_sse4.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 8%] Building CXX object tests/align/CMakeFiles/test_align_simd_local_variable_length_sse4.dir/test_align_simd_local_variable_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -msse4 -o CMakeFiles/test_align_simd_local_variable_length_sse4.dir/test_align_simd_local_variable_length.cpp.o -c /<>/tests/align/test_align_simd_local_variable_length.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_local_variable_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_local.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_local.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_local_variable_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_local_variable_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_local.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_local.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_local_variable_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_equal_length.cpp:36: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_equal_length.cpp:39: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_equal_length.cpp:36: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_equal_length.cpp:39: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ [ 8%] Linking CXX executable ../../bin/test_align_simd_local_variable_length_sse4 cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_local_variable_length_sse4.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_local_variable_length_sse4.dir/test_align_simd_local_variable_length.cpp.o -o ../../bin/test_align_simd_local_variable_length_sse4 -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 8%] Built target test_align_simd_local_variable_length_sse4 make -f tests/align/CMakeFiles/test_align_simd_global_equal_length_avx2.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length_avx2.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length_avx2.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_global_equal_length_avx2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_global_equal_length_avx2.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length_avx2.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 8%] Building CXX object tests/align/CMakeFiles/test_align_simd_global_equal_length_avx2.dir/test_align_simd_global_equal_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -mavx2 -o CMakeFiles/test_align_simd_global_equal_length_avx2.dir/test_align_simd_global_equal_length.cpp.o -c /<>/tests/align/test_align_simd_global_equal_length.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_equal_length.cpp:36: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_equal_length.cpp:39: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_equal_length.cpp:36: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_equal_length.cpp:39: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ [ 8%] Linking CXX executable ../../bin/test_align_simd_global_equal_length_sse4 cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_global_equal_length_sse4.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_global_equal_length_sse4.dir/test_align_simd_global_equal_length.cpp.o -o ../../bin/test_align_simd_global_equal_length_sse4 -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 8%] Built target test_align_simd_global_equal_length_sse4 make -f tests/align/CMakeFiles/test_align_simd_global_variable_length_avx2.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length_avx2.dir/depend make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tests/align /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tests/align /<>/obj-x86_64-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length_avx2.dir/DependInfo.cmake --color= Scanning dependencies of target test_align_simd_global_variable_length_avx2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_global_variable_length_avx2.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length_avx2.dir/build make[4]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 8%] Building CXX object tests/align/CMakeFiles/test_align_simd_global_variable_length_avx2.dir/test_align_simd_global_variable_length.cpp.o cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<>/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -mavx2 -o CMakeFiles/test_align_simd_global_variable_length_avx2.dir/test_align_simd_global_variable_length.cpp.o -c /<>/tests/align/test_align_simd_global_variable_length.cpp In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_variable_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:91:36: required from ‘void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:80:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_variable_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /<>/include/seqan/basic/basic_fundamental.h:82, from /<>/include/seqan/basic.h:58, from /<>/tests/align/test_align_simd_global_variable_length.cpp:35: /<>/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’: /<>/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]’ /<>/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /<>/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = long unsigned int; TExpand = seqan::TagGenerous_]’ /<>/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /<>/include/seqan/sequence/string_set_base.h:1301:18: required from ‘typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = long unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = long unsigned int]’ /<>/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = long unsigned int; typename seqan::Size::Type = long unsigned int]’ /<>/tests/align/test_align_simd_base.h:166:11: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]’ /<>/tests/align/test_align_simd_base.h:216:33: required from ‘void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]’ /<>/tests/align/test_align_simd_global.h:74:30: required from ‘void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]’ /<>/tests/align/test_align_simd_global.h:68:1: required from here /<>/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /<>/include/seqan/align.h:97, from /<>/tests/align/test_align_simd_base.h:41, from /<>/tests/align/test_align_simd_global_variable_length.cpp:38: /<>/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make[4]: *** [tests/align/CMakeFiles/test_align_simd_global_variable_length_avx2.dir/build.make:85: tests/align/CMakeFiles/test_align_simd_global_variable_length_avx2.dir/test_align_simd_global_variable_length.cpp.o] Error 1 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:3222: tests/align/CMakeFiles/test_align_simd_global_variable_length_avx2.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [ 8%] Linking CXX executable ../../bin/test_align_simd_global_equal_length_avx2 cd /<>/obj-x86_64-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_global_equal_length_avx2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_global_equal_length_avx2.dir/test_align_simd_global_equal_length.cpp.o -o ../../bin/test_align_simd_global_equal_length_avx2 -lrt -lz -lbz2 make[4]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 8%] Built target test_align_simd_global_equal_length_avx2 make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[2]: *** [Makefile:163: all] Error 2 make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j2 "INSTALL=install --strip-program=true" returned exit code 2 make[1]: *** [debian/rules:72: override_dh_auto_build-arch] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:43: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-10-05T20:14:55Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 6089648 Build-Time: 5842 Distribution: sid Fail-Stage: build Host Architecture: amd64 Install-Time: 20 Job: /srv/debomatic/incoming/seqan2_2.4.0+dfsg-12.dsc Machine Architecture: amd64 Package: seqan2 Package-Time: 5875 Source-Version: 2.4.0+dfsg-12 Space: 6089648 Status: attempted Version: 2.4.0+dfsg-12 -------------------------------------------------------------------------------- Finished at 2020-10-05T20:14:55Z Build needed 01:37:55, 6089648k disk space