sbuild (Debian sbuild) 0.79.1 (22 April 2020) on carme.larted.org.uk +==============================================================================+ | pbbam 1.0.6+dfsg-2 (amd64) Mon, 05 Oct 2020 09:14:11 +0000 | +==============================================================================+ Package: pbbam Version: 1.0.6+dfsg-2 Source Version: 1.0.6+dfsg-2 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-159a1311-b352-4d33-ae60-0c20edce7ed0' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup pbbam_1.0.6+dfsg-2 sid amd64 --------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup pbbam_1.0.6+dfsg-2 sid amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/pbbam-9wvKqX/resolver-g7UuAi' 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:4 http://localhost:3142/debian unstable/main amd64 Packages 2020-10-05-0800.58.pdiff [4170 B] Get:5 http://localhost:3142/debian sid/main Sources.diff/Index [27.9 kB] Get:6 http://localhost:3142/debian sid/main Sources 2020-10-05-0800.58.pdiff [7387 B] Get:6 http://localhost:3142/debian sid/main Sources 2020-10-05-0800.58.pdiff [7387 B] Fetched 360 kB in 2s (221 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/pbbam_1.0.6+dfsg-2.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/pbbam-9wvKqX/pbbam-1.0.6+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-9wvKqX' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>= 1.3.0), python3-cram, libgtest-dev, samtools, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>= 1.3.0), python3-cram, libgtest-dev, samtools, build-essential, fakeroot 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 [471 B] Get:5 copy:/<>/apt_archive ./ Packages [542 B] Fetched 1970 B in 0s (104 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 d-shlibs debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dpkg-dev dwz fakeroot file g++ g++-10 gcc gcc-10 gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libarchive13 libasan5 libasan6 libboost-dev libboost1.71-dev libbrotli1 libc6-dev libcroco3 libcrypt-dev libcurl3-gnutls libcurl4 libdebhelper-perl libdeflate0 libdpkg-perl libelf1 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgcc-10-dev libgcc-9-dev libglib2.0-0 libgssapi-krb5-2 libgtest-dev libhts-dev libhts3 libicu67 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpbcopper-dev libpbcopper1.6.0 libperl5.30 libpipeline1 libprocps8 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1 libstdc++-10-dev libstdc++-9-dev libsub-override-perl libtool libubsan1 libuchardet0 libuv1 libxml2 m4 man-db meson mime-support ninja-build perl perl-modules-5.30 pkg-config po-debconf procps python3 python3-cram python3-minimal python3-pkg-resources python3.8 python3.8-minimal samtools sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc 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 liblzma-doc libssl-doc libstdc++-10-doc libstdc++-9-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-setuptools python3.8-venv python3.8-doc binfmt-support cwltool Recommended packages: libalgorithm-merge-perl curl | wget | lynx ca-certificates libfile-fcntllock-perl liblocale-gettext-perl libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl psmisc The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils build-essential cmake cmake-data d-shlibs debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dpkg-dev dwz fakeroot file g++ g++-10 gcc gcc-10 gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libarchive13 libasan5 libasan6 libboost-dev libboost1.71-dev libbrotli1 libc6-dev libcroco3 libcrypt-dev libcurl3-gnutls libcurl4 libdebhelper-perl libdeflate0 libdpkg-perl libelf1 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgcc-10-dev libgcc-9-dev libglib2.0-0 libgssapi-krb5-2 libgtest-dev libhts-dev libhts3 libicu67 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpbcopper-dev libpbcopper1.6.0 libperl5.30 libpipeline1 libprocps8 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1 libstdc++-10-dev libstdc++-9-dev libsub-override-perl libtool libubsan1 libuchardet0 libuv1 libxml2 m4 man-db meson mime-support ninja-build perl perl-modules-5.30 pkg-config po-debconf procps python3 python3-cram python3-minimal python3-pkg-resources python3.8 python3.8-minimal samtools sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 106 newly installed, 0 to remove and 0 not upgraded. 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amd64 9.3.0-18 [2347 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libstdc++-9-dev amd64 9.3.0-18 [1702 kB] Get:89 http://localhost:3142/debian unstable/main amd64 libboost1.71-dev amd64 1.71.0-6+b2 [9097 kB] Get:90 http://localhost:3142/debian unstable/main amd64 libboost-dev amd64 1.71.0.3 [4340 B] Get:91 http://localhost:3142/debian unstable/main amd64 libcurl3-gnutls amd64 7.72.0-1 [333 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libdeflate0 amd64 1.6-1 [55.1 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libgtest-dev amd64 1.10.0-3 [1580 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libhts3 amd64 1.11-1 [366 kB] Get:95 http://localhost:3142/debian unstable/main amd64 liblzma-dev amd64 5.2.4-1+b1 [211 kB] Get:96 http://localhost:3142/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:97 http://localhost:3142/debian unstable/main amd64 libhts-dev amd64 1.11-1 [4132 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libpbcopper1.6.0 amd64 1.6.0+dfsg-4+b1 [354 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libpbcopper-dev amd64 1.6.0+dfsg-4+b1 [597 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libssl-dev amd64 1.1.1g-1 [1802 kB] Get:101 http://localhost:3142/debian unstable/main amd64 ninja-build amd64 1.10.1-1 [112 kB] Get:102 http://localhost:3142/debian unstable/main amd64 python3-pkg-resources all 49.3.1-2 [188 kB] Get:103 http://localhost:3142/debian unstable/main amd64 meson all 0.55.3-1 [416 kB] Get:104 http://localhost:3142/debian unstable/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get:105 http://localhost:3142/debian unstable/main amd64 python3-cram all 0.7-4 [17.3 kB] Get:106 http://localhost:3142/debian unstable/main amd64 samtools amd64 1.11-1 [545 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 104 MB in 1s (125 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 libssl1.1:amd64 (1.1.1g-1) ... Setting up libpython3.8-minimal:amd64 (3.8.6-1) ... Setting up libexpat1:amd64 (2.2.10-1) ... Setting up python3.8-minimal (3.8.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13299 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.8.2-3_amd64.deb ... Unpacking python3-minimal (3.8.2-3) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.64_all.deb ... Unpacking mime-support (3.64) ... Selecting previously unselected package libpython3.8-stdlib:amd64. Preparing to unpack .../libpython3.8-stdlib_3.8.6-1_amd64.deb ... Unpacking libpython3.8-stdlib:amd64 (3.8.6-1) ... Selecting previously unselected package python3.8. Preparing to unpack .../python3.8_3.8.6-1_amd64.deb ... Unpacking python3.8 (3.8.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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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 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 libstdc++-9-dev:amd64 (9.3.0-18) ... Setting up libtool (2.4.6-14) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.2.1) ... Setting up libboost1.71-dev:amd64 (1.71.0-6+b2) ... Setting up meson (0.55.3-1) ... Setting up libcurl3-gnutls:amd64 (7.72.0-1) ... 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 pkg-config (0.29.2-1) ... 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 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 libhts3:amd64 (1.11-1) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.11-1) ... Setting up samtools (1.11-1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.2.1) ... Setting up dh-exec (0.23.2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | 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++-9-dev_9.3.0-18 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 d-shlibs_0.94 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-exec_0.23.2 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 googletest_1.10.0-3 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 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 libasan5_9.3.0-18 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 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 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 libcurl3-gnutls_7.72.0-1 libcurl4_7.72.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdeflate0_1.6-1 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-9-dev_9.3.0-18 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 libgtest-dev_1.10.0-3 libhogweed4_3.5.1+really3.4.1-1 libhogweed6_3.6-2 libhts-dev_1.11-1 libhts3_1.11-1 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 liblsan0_10.2.0-13 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1+b1 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 libpbcopper-dev_1.6.0+dfsg-4+b1 libpbcopper1.6.0_1.6.0+dfsg-4+b1 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 libssl-dev_1.1.1g-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-13 libstdc++-9-dev_9.3.0-18 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 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 meson_0.55.3-1 mime-support_3.64 mount_2.36-3+b1 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 ninja-build_1.10.1-1 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 pkg-config_0.29.2-1 po-debconf_1.0.21 procps_2:3.3.16-5 python3_3.8.2-3 python3-cram_0.7-4 python3-minimal_3.8.2-3 python3-pkg-resources_49.3.1-2 python3.8_3.8.6-1 python3.8-minimal_3.8.6-1 readline-common_8.0-4 samtools_1.11-1 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: pbbam Binary: pbbamtools, libpbbam1.0.6, libpbbam-dev Architecture: any Version: 1.0.6+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://pbbam.readthedocs.org/en/latest/index.html Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/pbbam Vcs-Git: https://salsa.debian.org/med-team/pbbam.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 12), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>= 1.3.0), python3-cram, libgtest-dev , samtools Package-List: libpbbam-dev deb libdevel optional arch=any libpbbam1.0.6 deb libs optional arch=any pbbamtools deb science optional arch=any Checksums-Sha1: 4050512da50665f38825a0855aa916ef1b7812b4 7754752 pbbam_1.0.6+dfsg.orig.tar.xz d1b9d2d0d8450744e69516e6200c551865dab6a7 8500 pbbam_1.0.6+dfsg-2.debian.tar.xz Checksums-Sha256: 1b4757d6c5e8e651029a643ddbbb86a305bff6da97100b5fad6a735aa7ddfb32 7754752 pbbam_1.0.6+dfsg.orig.tar.xz c5821fa148212910ac232969ed29d13923f69ed8a2c418f1011815ec03e6743c 8500 pbbam_1.0.6+dfsg-2.debian.tar.xz Files: 5227d4ac07c92db02683b8154114a6bf 7754752 pbbam_1.0.6+dfsg.orig.tar.xz e35df252db182b40ce710114c60089bc 8500 pbbam_1.0.6+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl3+EbARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEpBA//WvLoA6AGJPUWL+3SFbBB9r8mpbK+bei1 7CbM/R/i8GPJpYNMuMLrMZ7zfYABgxQ0hIyieGg8ALD8tepFD6uMbAzXO7uWFkZs DxLFEbwDEx1G57SWFWFc3ix4yondgfyIUS9PkUlAm5A5i9EhLi6n9YlOgdNZrFk3 u5fevGGH5E9kP1ek+r1mzStMAnLnSLRghax8mIyJlv+vZHQWGXTat+s5EXj8fXOT u840bZRQk+4cFqtfloalCBPaEwy5ELliUgwojp2odpW/Gz1W/l6cA9rR+VHQHlka Qu+aOIRLHooCXZv9B/BRq4AbLuMxojvkzH7nmoVmCIert5oI61986Ye4GSys/DNH dTaVZeqqp1QHFGz4cOmmYBgZ67BvLEtzJzdp1I2Qha5NnxHvCdCaouCpxFfsCEtq eD+AnvHUwKKAiQvhfGYr7Ug+un2PN/8TZo6nW1G0Fmw/Uwsqw5DeiqIQ9jx8Pg4T x72XAMZTlgselTMA7rFDt8VZZj2Lrv6qSgUxq9A3fLTRAe4C9ikngCOQQ4zHeiXU 6ECd9Q/Juj0iFAHBohTl4njckme3ywhv0UE1cJgdVTs2V1GjjO7s5VEnY3dFbR3y V30w26IONzra/a04jqSTMRHTYZLAtW+KQTRYFlmPdxArAezogjyNEI7Wow7lUvSe cd0a8km4nwo= =di4N -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.Ku0K3fvC/trustedkeys.kbx': General error gpgv: Signature made Sat Dec 21 12:36:00 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pbbam_1.0.6+dfsg-2.dsc dpkg-source: info: extracting pbbam in /<> dpkg-source: info: unpacking pbbam_1.0.6+dfsg.orig.tar.xz dpkg-source: info: unpacking pbbam_1.0.6+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_gtest_depcheck.patch dpkg-source: info: applying use_debian_packaged_python3-cram.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying results_with_latest_samtools.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network pbbam_1.0.6+dfsg-2 sid amd64 --------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network pbbam_1.0.6+dfsg-2 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-159a1311-b352-4d33-ae60-0c20edce7ed0 SCHROOT_UID=1001 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic XDG_RUNTIME_DIR=/run/user/1001 XDG_SESSION_CLASS=background XDG_SESSION_ID=c3970972 XDG_SESSION_TYPE=unspecified dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 1.0.6+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --buildsystem=meson debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /<>/gendata make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building pbbam using existing ./pbbam_1.0.6+dfsg.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building pbbam in pbbam_1.0.6+dfsg-2.debian.tar.xz dpkg-source: info: building pbbam in pbbam_1.0.6+dfsg-2.dsc debian/rules build dh build --buildsystem=meson dh_update_autotools_config -O--buildsystem=meson dh_autoreconf -O--buildsystem=meson dh_auto_configure -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu The Meson build system Version: 0.55.3 Source dir: /<> Build dir: /<>/obj-x86_64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 1.0.6 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' C++ compiler for the host machine: c++ (gcc 10.2.0 "c++ (Debian 10.2.0-13) 10.2.0") C++ linker for the host machine: c++ ld.bfd 2.35.1 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: YES Compiler for C++ supports arguments -Wduplicated-branches: YES Compiler for C++ supports arguments -Wlogical-op: YES Compiler for C++ supports arguments -Wrestrict: YES Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: YES Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: YES Run-time dependency threads found: YES Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency Boost found: YES 1.71.0 (/usr/include) Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.11-1 Run-time dependency pbcopper found: YES 1.6.0 Program python3 found: YES Program tools/check-formatting found: YES Program cram3 found: YES WARNING: Project targeting '>= 0.46.0' but tried to use feature introduced in '0.53.0': Fallback without variable name. Run-time dependency GTest found: YES 1.10.0 Configuring group.fofn using configuration Configuring PbbamTestData.h using configuration Configuring synthetic_movie_all.subreadset.xml using configuration Configuring Bam2SamVersion.h using configuration Configuring bam2sam.t using configuration Configuring PbIndexVersion.h using configuration Configuring PbIndexDumpVersion.h using configuration Configuring pbindexdump_json.t using configuration Configuring pbindexdump_cpp.t using configuration Configuring PbMergeVersion.h using configuration Configuring pbmerge_pacbio_ordering.t using configuration Configuring pbmerge_aligned_ordering.t using configuration Configuring pbmerge_mixed_ordering.t using configuration Configuring pbmerge_dataset.t using configuration Configuring pbmerge_fofn.t using configuration Configuring PbBamifyVersion.h using configuration Program samtools found: YES Configuring pbbamify.t using configuration Build targets in project: 8 WARNING: Project specifies a minimum meson_version '>= 0.46.0' but uses features which were added in newer versions: * 0.53.0: {'Fallback without variable name'} Option buildtype is: plain [default: release] Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.1.0.6.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.1.0.6.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp [2/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamFile.cpp.o -MF src/libpbbam.so.1.0.6.p/BamFile.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamFile.cpp.o -c ../src/BamFile.cpp [3/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BaiIndexedBamReader.cpp.o -MF src/libpbbam.so.1.0.6.p/BaiIndexedBamReader.cpp.o.d -o src/libpbbam.so.1.0.6.p/BaiIndexedBamReader.cpp.o -c ../src/BaiIndexedBamReader.cpp [4/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BaiIndexCache.cpp.o -MF src/libpbbam.so.1.0.6.p/BaiIndexCache.cpp.o.d -o src/libpbbam.so.1.0.6.p/BaiIndexCache.cpp.o -c ../src/BaiIndexCache.cpp [5/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamReader.cpp.o -MF src/libpbbam.so.1.0.6.p/BamReader.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamReader.cpp.o -c ../src/BamReader.cpp [6/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamFileMerger.cpp.o -MF src/libpbbam.so.1.0.6.p/BamFileMerger.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamFileMerger.cpp.o -c ../src/BamFileMerger.cpp [7/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamRecordBuilder.cpp.o -MF src/libpbbam.so.1.0.6.p/BamRecordBuilder.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamRecordBuilder.cpp.o -c ../src/BamRecordBuilder.cpp [8/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamRecordTags.cpp.o -MF src/libpbbam.so.1.0.6.p/BamRecordTags.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamRecordTags.cpp.o -c ../src/BamRecordTags.cpp [9/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamHeader.cpp.o -MF src/libpbbam.so.1.0.6.p/BamHeader.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamHeader.cpp.o -c ../src/BamHeader.cpp [10/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamRecordView.cpp.o -MF src/libpbbam.so.1.0.6.p/BamRecordView.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamRecordView.cpp.o -c ../src/BamRecordView.cpp [11/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamRecordImpl.cpp.o -MF src/libpbbam.so.1.0.6.p/BamRecordImpl.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamRecordImpl.cpp.o -c ../src/BamRecordImpl.cpp ../src/BamRecordImpl.cpp: In member function ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::operator=(const PacBio::BAM::BamRecordImpl&)’: ../src/BamRecordImpl.cpp:90:18: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 90 | bam_copy1(d_.get(), other.d_.get()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/BamRecordImpl.cpp: In static member function ‘static PacBio::BAM::BamRecordImpl PacBio::BAM::BamRecordImpl::FromRawData(const std::shared_ptr&)’: ../src/BamRecordImpl.cpp:234:14: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 234 | bam_copy1(result.d_.get(), rawData.get()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [12/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamRecord.cpp.o -MF src/libpbbam.so.1.0.6.p/BamRecord.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamRecord.cpp.o -c ../src/BamRecord.cpp [13/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamWriter.cpp.o -MF src/libpbbam.so.1.0.6.p/BamWriter.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamWriter.cpp.o -c ../src/BamWriter.cpp [14/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BamTagCodec.cpp.o -MF src/libpbbam.so.1.0.6.p/BamTagCodec.cpp.o.d -o src/libpbbam.so.1.0.6.p/BamTagCodec.cpp.o -c ../src/BamTagCodec.cpp [15/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BgzipFastaWriter.cpp.o -MF src/libpbbam.so.1.0.6.p/BgzipFastaWriter.cpp.o.d -o src/libpbbam.so.1.0.6.p/BgzipFastaWriter.cpp.o -c ../src/BgzipFastaWriter.cpp [16/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong 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src/libpbbam.so.1.0.6.p/BgzipFastqWriter.cpp.o -c ../src/BgzipFastqWriter.cpp [18/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/ChemistryTable.cpp.o -MF src/libpbbam.so.1.0.6.p/ChemistryTable.cpp.o.d -o src/libpbbam.so.1.0.6.p/ChemistryTable.cpp.o -c ../src/ChemistryTable.cpp [19/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/Config.cpp.o -MF src/libpbbam.so.1.0.6.p/Config.cpp.o.d -o src/libpbbam.so.1.0.6.p/Config.cpp.o -c ../src/Config.cpp [20/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/BarcodeQuery.cpp.o -MF src/libpbbam.so.1.0.6.p/BarcodeQuery.cpp.o.d -o src/libpbbam.so.1.0.6.p/BarcodeQuery.cpp.o -c ../src/BarcodeQuery.cpp [21/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/Compare.cpp.o -MF src/libpbbam.so.1.0.6.p/Compare.cpp.o.d -o src/libpbbam.so.1.0.6.p/Compare.cpp.o -c ../src/Compare.cpp [22/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/CompositeFastaReader.cpp.o -MF src/libpbbam.so.1.0.6.p/CompositeFastaReader.cpp.o.d -o src/libpbbam.so.1.0.6.p/CompositeFastaReader.cpp.o -c ../src/CompositeFastaReader.cpp [23/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/DataSetElement.cpp.o -MF src/libpbbam.so.1.0.6.p/DataSetElement.cpp.o.d -o src/libpbbam.so.1.0.6.p/DataSetElement.cpp.o -c ../src/DataSetElement.cpp [24/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include 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-I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/MD5.cpp.o -MF src/libpbbam.so.1.0.6.p/MD5.cpp.o.d -o src/libpbbam.so.1.0.6.p/MD5.cpp.o -c ../src/MD5.cpp [53/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/IndexedFastqReader.cpp.o -MF src/libpbbam.so.1.0.6.p/IndexedFastqReader.cpp.o.d -o src/libpbbam.so.1.0.6.p/IndexedFastqReader.cpp.o -c ../src/IndexedFastqReader.cpp [54/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/IndexedBamWriter.cpp.o -MF src/libpbbam.so.1.0.6.p/IndexedBamWriter.cpp.o.d -o src/libpbbam.so.1.0.6.p/IndexedBamWriter.cpp.o -c ../src/IndexedBamWriter.cpp [55/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/KSeqReader.cpp.o -MF src/libpbbam.so.1.0.6.p/KSeqReader.cpp.o.d -o src/libpbbam.so.1.0.6.p/KSeqReader.cpp.o -c ../src/KSeqReader.cpp [56/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/MemoryUtils.cpp.o -MF src/libpbbam.so.1.0.6.p/MemoryUtils.cpp.o.d -o src/libpbbam.so.1.0.6.p/MemoryUtils.cpp.o -c ../src/MemoryUtils.cpp ../src/MemoryUtils.cpp: In static member function ‘static std::shared_ptr PacBio::BAM::BamHeaderMemory::MakeRawHeader(const PacBio::BAM::BamHeader&)’: ../src/MemoryUtils.cpp:32:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] 32 | rawData->cigar_tab = nullptr; | ^~~~~~~~~ In file included from ../src/MemoryUtils.h:13, from ../src/MemoryUtils.cpp:5: /usr/include/htslib/sam.h:75:19: note: declared here 75 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^~~~~~~~~ ../src/MemoryUtils.cpp:32:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] 32 | rawData->cigar_tab = nullptr; | ^~~~~~~~~ In file included from ../src/MemoryUtils.h:13, from ../src/MemoryUtils.cpp:5: /usr/include/htslib/sam.h:75:19: note: declared here 75 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^~~~~~~~~ ../src/MemoryUtils.cpp:32:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] 32 | rawData->cigar_tab = nullptr; | ^~~~~~~~~ In file included from ../src/MemoryUtils.h:13, from ../src/MemoryUtils.cpp:5: /usr/include/htslib/sam.h:75:19: note: declared here 75 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^~~~~~~~~ [57/216] c++ -Isrc/libpbbam.so.1.0.6.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.0.6.p/PbiFile.cpp.o -MF 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src/libpbbam.so.1.0.6 src/libpbbam.so.1.0.6.p/AlignmentPrinter.cpp.o src/libpbbam.so.1.0.6.p/BaiIndexCache.cpp.o src/libpbbam.so.1.0.6.p/BaiIndexedBamReader.cpp.o src/libpbbam.so.1.0.6.p/BamFile.cpp.o src/libpbbam.so.1.0.6.p/BamFileMerger.cpp.o src/libpbbam.so.1.0.6.p/BamHeader.cpp.o src/libpbbam.so.1.0.6.p/BamReader.cpp.o src/libpbbam.so.1.0.6.p/BamRecord.cpp.o src/libpbbam.so.1.0.6.p/BamRecordBuilder.cpp.o src/libpbbam.so.1.0.6.p/BamRecordImpl.cpp.o src/libpbbam.so.1.0.6.p/BamRecordTags.cpp.o src/libpbbam.so.1.0.6.p/BamRecordView.cpp.o src/libpbbam.so.1.0.6.p/BamTagCodec.cpp.o src/libpbbam.so.1.0.6.p/BamWriter.cpp.o src/libpbbam.so.1.0.6.p/BarcodeQuery.cpp.o src/libpbbam.so.1.0.6.p/BgzipFastaWriter.cpp.o src/libpbbam.so.1.0.6.p/BgzipFastqWriter.cpp.o src/libpbbam.so.1.0.6.p/BgzipWriter.cpp.o src/libpbbam.so.1.0.6.p/ChemistryTable.cpp.o src/libpbbam.so.1.0.6.p/Compare.cpp.o src/libpbbam.so.1.0.6.p/CompositeFastaReader.cpp.o src/libpbbam.so.1.0.6.p/Config.cpp.o src/libpbbam.so.1.0.6.p/DataSet.cpp.o src/libpbbam.so.1.0.6.p/DataSetBaseTypes.cpp.o src/libpbbam.so.1.0.6.p/DataSetElement.cpp.o src/libpbbam.so.1.0.6.p/DataSetIO.cpp.o src/libpbbam.so.1.0.6.p/DataSetTypes.cpp.o src/libpbbam.so.1.0.6.p/DataSetXsd.cpp.o src/libpbbam.so.1.0.6.p/EntireFileQuery.cpp.o src/libpbbam.so.1.0.6.p/FaiIndex.cpp.o src/libpbbam.so.1.0.6.p/FaiZmwChunker.cpp.o src/libpbbam.so.1.0.6.p/FastaCache.cpp.o src/libpbbam.so.1.0.6.p/FastaReader.cpp.o src/libpbbam.so.1.0.6.p/FastaSequence.cpp.o src/libpbbam.so.1.0.6.p/FastaSequenceQuery.cpp.o src/libpbbam.so.1.0.6.p/FastaWriter.cpp.o src/libpbbam.so.1.0.6.p/FastqReader.cpp.o src/libpbbam.so.1.0.6.p/FastqSequence.cpp.o src/libpbbam.so.1.0.6.p/FastqWriter.cpp.o src/libpbbam.so.1.0.6.p/FileProducer.cpp.o src/libpbbam.so.1.0.6.p/FileUtils.cpp.o src/libpbbam.so.1.0.6.p/FofnReader.cpp.o src/libpbbam.so.1.0.6.p/FormatUtils.cpp.o src/libpbbam.so.1.0.6.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.1.0.6.p/IFastaWriter.cpp.o src/libpbbam.so.1.0.6.p/IFastqWriter.cpp.o src/libpbbam.so.1.0.6.p/IndexedBamWriter.cpp.o src/libpbbam.so.1.0.6.p/IndexedFastaReader.cpp.o src/libpbbam.so.1.0.6.p/IndexedFastqBgzfReader.cpp.o src/libpbbam.so.1.0.6.p/IndexedFastqReader.cpp.o src/libpbbam.so.1.0.6.p/IndexedFastqTextReader.cpp.o src/libpbbam.so.1.0.6.p/IndexedFastqReaderImpl.cpp.o src/libpbbam.so.1.0.6.p/IRecordWriter.cpp.o src/libpbbam.so.1.0.6.p/KSeqReader.cpp.o src/libpbbam.so.1.0.6.p/MD5.cpp.o src/libpbbam.so.1.0.6.p/MemoryUtils.cpp.o src/libpbbam.so.1.0.6.p/PbiBuilder.cpp.o src/libpbbam.so.1.0.6.p/PbiFile.cpp.o src/libpbbam.so.1.0.6.p/PbiFilter.cpp.o src/libpbbam.so.1.0.6.p/PbiFilterQuery.cpp.o src/libpbbam.so.1.0.6.p/PbiFilterTypes.cpp.o src/libpbbam.so.1.0.6.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.1.0.6.p/PbiIndexIO.cpp.o src/libpbbam.so.1.0.6.p/PbiRawData.cpp.o src/libpbbam.so.1.0.6.p/ProgramInfo.cpp.o src/libpbbam.so.1.0.6.p/QNameQuery.cpp.o src/libpbbam.so.1.0.6.p/ReadAccuracyQuery.cpp.o src/libpbbam.so.1.0.6.p/ReadGroupInfo.cpp.o src/libpbbam.so.1.0.6.p/RecordType.cpp.o src/libpbbam.so.1.0.6.p/SamTagCodec.cpp.o src/libpbbam.so.1.0.6.p/SamWriter.cpp.o src/libpbbam.so.1.0.6.p/SequenceInfo.cpp.o src/libpbbam.so.1.0.6.p/StringUtilities.cpp.o src/libpbbam.so.1.0.6.p/SubreadLengthQuery.cpp.o src/libpbbam.so.1.0.6.p/Tag.cpp.o src/libpbbam.so.1.0.6.p/TagCollection.cpp.o src/libpbbam.so.1.0.6.p/TextFileReader.cpp.o src/libpbbam.so.1.0.6.p/TextFileWriter.cpp.o src/libpbbam.so.1.0.6.p/Validator.cpp.o src/libpbbam.so.1.0.6.p/ValidationErrors.cpp.o src/libpbbam.so.1.0.6.p/ValidationException.cpp.o src/libpbbam.so.1.0.6.p/Version.cpp.o src/libpbbam.so.1.0.6.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.1.0.6.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.1.0.6.p/VirtualZmwReader.cpp.o src/libpbbam.so.1.0.6.p/VirtualRegion.cpp.o src/libpbbam.so.1.0.6.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.1.0.6.p/XmlReader.cpp.o src/libpbbam.so.1.0.6.p/XmlWriter.cpp.o src/libpbbam.so.1.0.6.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.1.0.6.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.1.0.6.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.1.0.6.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.1.0.6.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.1.0.6.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.1.0.6.p/ZmwGroupQuery.cpp.o src/libpbbam.so.1.0.6.p/ZmwReadStitcher.cpp.o src/libpbbam.so.1.0.6.p/ZmwQuery.cpp.o src/libpbbam.so.1.0.6.p/ZmwTypeMap.cpp.o src/libpbbam.so.1.0.6.p/bed_BedReader.cpp.o src/libpbbam.so.1.0.6.p/bed_BedWriter.cpp.o src/libpbbam.so.1.0.6.p/ccs_CCSPbiBuilder.cpp.o src/libpbbam.so.1.0.6.p/ccs_CCSRecordFormat.cpp.o src/libpbbam.so.1.0.6.p/ccs_CCSRecordReader.cpp.o src/libpbbam.so.1.0.6.p/ccs_CCSRecordWriter.cpp.o src/libpbbam.so.1.0.6.p/vcf_VcfFile.cpp.o src/libpbbam.so.1.0.6.p/vcf_VcfFormat.cpp.o src/libpbbam.so.1.0.6.p/vcf_VcfHeader.cpp.o src/libpbbam.so.1.0.6.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.1.0.6.p/vcf_VcfQuery.cpp.o src/libpbbam.so.1.0.6.p/vcf_VcfReader.cpp.o src/libpbbam.so.1.0.6.p/vcf_VcfSort.cpp.o src/libpbbam.so.1.0.6.p/vcf_VcfVariant.cpp.o src/libpbbam.so.1.0.6.p/vcf_VcfWriter.cpp.o src/libpbbam.so.1.0.6.p/pugixml_pugixml.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.1.0.6 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [124/216] /usr/bin/meson --internal symbolextractor /<>/obj-x86_64-linux-gnu src/libpbbam.so.1.0.6 src/libpbbam.so.1.0.6 src/libpbbam.so.1.0.6.p/libpbbam.so.1.0.6.symbols [125/216] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamHeader.cpp.o -MF tests/pbbam_test.p/src_test_BamHeader.cpp.o.d -o tests/pbbam_test.p/src_test_BamHeader.cpp.o -c ../tests/src/test_BamHeader.cpp ../tests/src/test_BamHeader.cpp: In member function ‘virtual void BamHeaderTest_ConvertToRawDataOk_Test::TestBody()’: ../tests/src/test_BamHeader.cpp:197:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] 197 | rawData->cigar_tab = nullptr; | ^~~~~~~~~ In file included from ../tests/src/test_BamHeader.cpp:9: /usr/include/htslib/sam.h:75:19: note: declared here 75 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^~~~~~~~~ ../tests/src/test_BamHeader.cpp:197:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] 197 | rawData->cigar_tab = nullptr; | ^~~~~~~~~ In file included from ../tests/src/test_BamHeader.cpp:9: /usr/include/htslib/sam.h:75:19: note: declared here 75 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^~~~~~~~~ ../tests/src/test_BamHeader.cpp:197:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] 197 | rawData->cigar_tab = nullptr; | ^~~~~~~~~ In file included from ../tests/src/test_BamHeader.cpp:9: /usr/include/htslib/sam.h:75:19: note: declared here 75 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^~~~~~~~~ ../tests/src/test_BamHeader.cpp: In member function ‘virtual void BamHeaderTest_ExtractFromRawDataOk_Test::TestBody()’: ../tests/src/test_BamHeader.cpp:251:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] 251 | rawData->cigar_tab = nullptr; | ^~~~~~~~~ In file included from ../tests/src/test_BamHeader.cpp:9: /usr/include/htslib/sam.h:75:19: note: declared here 75 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^~~~~~~~~ ../tests/src/test_BamHeader.cpp:251:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] 251 | rawData->cigar_tab = nullptr; | ^~~~~~~~~ In file included from ../tests/src/test_BamHeader.cpp:9: /usr/include/htslib/sam.h:75:19: note: declared here 75 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^~~~~~~~~ ../tests/src/test_BamHeader.cpp:251:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations] 251 | rawData->cigar_tab = nullptr; | ^~~~~~~~~ In file included from ../tests/src/test_BamHeader.cpp:9: /usr/include/htslib/sam.h:75:19: note: declared here 75 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead"); | ^~~~~~~~~ [126/216] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordBuilder.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordBuilder.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordBuilder.cpp.o -c ../tests/src/test_BamRecordBuilder.cpp [127/216] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -c ../tests/src/test_BamRecordImplTags.cpp [128/216] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o -c ../tests/src/test_BamRecordImplCore.cpp ../tests/src/test_BamRecordImplCore.cpp: In lambda function: ../tests/src/test_BamRecordImplCore.cpp:279:18: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 279 | bam_copy1(PacBio::BAM::BamRecordMemory::GetRawData(result).get(), rawData.get()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [129/216] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecord.cpp.o -MF tests/pbbam_test.p/src_test_BamRecord.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecord.cpp.o -c ../tests/src/test_BamRecord.cpp [130/216] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamWriter.cpp.o -MF tests/pbbam_test.p/src_test_BamWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BamWriter.cpp.o -c ../tests/src/test_BamWriter.cpp FAILED: tests/pbbam_test.p/src_test_BamWriter.cpp.o c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamWriter.cpp.o -MF tests/pbbam_test.p/src_test_BamWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BamWriter.cpp.o -c ../tests/src/test_BamWriter.cpp ../tests/src/test_BamWriter.cpp: In function ‘void BamWriterTests::checkSingleRecord(bool)’: ../tests/src/test_BamWriter.cpp:40:34: error: call of overloaded ‘CigarData(const char [1])’ is ambiguous 40 | bamRecord.Impl().CigarData(""); | ^ In file included from ../include/pbbam/BamRecord.h:24, from ../tests/src/test_BamWriter.cpp:11: ../include/pbbam/BamRecordImpl.h:251:20: note: candidate: ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::CigarData(const Cigar&)’ 251 | BamRecordImpl& CigarData(const Cigar& cigar); | ^~~~~~~~~ ../include/pbbam/BamRecordImpl.h:258:20: note: candidate: ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::CigarData(const string&)’ 258 | BamRecordImpl& CigarData(const std::string& cigarString); | ^~~~~~~~~ [131/216] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o -c ../tests/src/test_BamRecordMapping.cpp [132/216] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o -c ../tests/src/test_BamRecordImplVariableData.cpp [133/216] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o -c ../tests/src/test_BamRecordClipping.cpp ninja: build stopped: subcommand failed. dh_auto_build: error: cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1 make: *** [debian/rules:13: build] Error 25 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-10-05T09:17:51Z 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: 381780 Build-Time: 196 Distribution: sid Fail-Stage: build Host Architecture: amd64 Install-Time: 20 Job: /srv/debomatic/incoming/pbbam_1.0.6+dfsg-2.dsc Machine Architecture: amd64 Package: pbbam Package-Time: 220 Source-Version: 1.0.6+dfsg-2 Space: 381780 Status: attempted Version: 1.0.6+dfsg-2 -------------------------------------------------------------------------------- Finished at 2020-10-05T09:17:51Z Build needed 00:03:40, 381780k disk space