sbuild (Debian sbuild) 0.91.5 (17 December 2025) on carme.larted.org.uk +==============================================================================+ | abyss 2.3.10-2 (amd64) Sun, 29 Mar 2026 04:02:04 +0000 | +==============================================================================+ Package: abyss Version: 2.3.10-2 Source Version: 2.3.10-2 Distribution: perl-5.42-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Sun, 29 Mar 2026 04:02:05 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup abyss_2.3.10-2 perl-5.42-throwaway amd64 --------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup abyss_2.3.10-2 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 29 Mar 2026 04:02:05 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Hit:3 http://deb.debian.org/debian sid InRelease 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 Sun, 29 Mar 2026 04:02:07 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/abyss_2.3.10-2.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 29 Mar 2026 04:02:07 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkgconf, help2man, debhelper, build-essential Filtered Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkgconf, help2man, debhelper, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/abyss-BQNOuM/resolver-v6GwZV/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/abyss-BQNOuM/resolver-v6GwZV/apt_archive ./ InRelease Get:2 copy:/build/abyss-BQNOuM/resolver-v6GwZV/apt_archive ./ Release [609 B] Ign:3 copy:/build/abyss-BQNOuM/resolver-v6GwZV/apt_archive ./ Release.gpg Get:4 copy:/build/abyss-BQNOuM/resolver-v6GwZV/apt_archive ./ Sources [777 B] Get:5 copy:/build/abyss-BQNOuM/resolver-v6GwZV/apt_archive ./ Packages [807 B] Fetched 2193 B in 0s (0 B/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... Solving dependencies... The following additional packages will be installed: architecture-properties autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran-15 gfortran-15-x86-64-linux-gnu groff-base help2man ibverbs-providers icu-devtools intltool-debian libamd-comgr3 libamdhip64-6 libarchive-zip-perl libboost-exception1.90-dev libboost-graph-dev libboost-graph1.90-dev libboost-graph1.90.0 libboost-regex1.90-dev libboost-regex1.90.0 libboost-serialization1.90-dev libboost-serialization1.90.0 libboost-test1.90-dev libboost-test1.90.0 libboost1.90-dev libbrotli1 libbtllib-dev libcbor0.10 libclang-common-21-dev libcom-err2 libcpptoml-dev libcurl3t64-gnutls libdebhelper-perl libdeflate0 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libfuse3-4 libgfortran-15-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhtml-parser-perl libhtml-tagset-perl libhts3t64 libhtscodecs2 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu78 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm21 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libpciaccess0 libpipeline1 libpkgconf7 libpmix2t64 libprrte-bin libprrte-dev libprrte3 libpsl5t64 libpsm2-2 librdmacm1t64 librtmp1 libsparsehash-dev libsqlite3-dev libssh2-1t64 libsystemd-shared libtext-markdown-perl libtext-multimarkdown-perl libtool libucc1 libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2-16 libxnvctrl0 libz3-4 libze1 m4 man-db mount ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkgconf pkgconf-bin po-debconf samtools sensible-utils systemd wget zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n gfortran-15-multilib gfortran-15-doc libcoarrays-dev groff graphviz libboost1.90-doc libboost-atomic1.90-dev libboost-chrono1.90-dev libboost-container1.90-dev libboost-context1.90-dev libboost-contract1.90-dev libboost-coroutine1.90-dev libboost-date-time1.90-dev libboost-fiber1.90-dev libboost-filesystem1.90-dev libboost-graph-parallel1.90-dev libboost-iostreams1.90-dev libboost-json1.90-dev libboost-locale1.90-dev libboost-log1.90-dev libboost-math1.90-dev libboost-mpi-python1.90-dev libboost-mpi1.90-dev libboost-nowide1.90-dev libboost-numpy1.90-dev libboost-program-options1.90-dev libboost-python1.90-dev libboost-random1.90-dev libboost-stacktrace1.90-dev libboost-thread1.90-dev libboost-timer1.90-dev libboost-type-erasure1.90-dev libboost-url1.90-dev libboost-wave1.90-dev libboost1.90-tools-dev libmpfrc++-dev libntl-dev fuse3 krb5-doc krb5-user libdata-dump-perl libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils sqlite3-doc libarchive13t64 libbpf1 libcryptsetup12 libdw1t64 libpwquality1 libqrencode4 libtss2-esys-3.0.2-0t64 libtss2-mu-4.0.1-0t64 libtss2-rc0t64 libtss2-tcti-device0t64 libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libwww-perl m4-doc apparmor less www-browser nfs-common opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl cwltool systemd-container systemd-homed systemd-userdbd systemd-boot systemd-resolved systemd-repart libtss2-tcti-device0 polkitd Recommended packages: libsdsl-dev libclang-rt-21-dev ca-certificates libarchive-cpio-perl libhttp-message-perl javascript-common krb5-locales libgpm2 libcoarrays-openmpi-dev libpmix-dev publicsuffix libapparmor1 libkmod2 xauth libmail-sendmail-perl default-dbus-system-bus | dbus-system-bus linux-sysctl-defaults login systemd-timesyncd | time-daemon systemd-cryptsetup The following NEW packages will be installed: architecture-properties autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran-15 gfortran-15-x86-64-linux-gnu groff-base help2man ibverbs-providers icu-devtools intltool-debian libamd-comgr3 libamdhip64-6 libarchive-zip-perl libboost-exception1.90-dev libboost-graph-dev libboost-graph1.90-dev libboost-graph1.90.0 libboost-regex1.90-dev libboost-regex1.90.0 libboost-serialization1.90-dev libboost-serialization1.90.0 libboost-test1.90-dev libboost-test1.90.0 libboost1.90-dev libbrotli1 libbtllib-dev libcbor0.10 libclang-common-21-dev libcom-err2 libcpptoml-dev libcurl3t64-gnutls libdebhelper-perl libdeflate0 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libevent-2.1-7t64 libevent-core-2.1-7t64 libevent-dev libevent-extra-2.1-7t64 libevent-openssl-2.1-7t64 libevent-pthreads-2.1-7t64 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libfuse3-4 libgfortran-15-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhtml-parser-perl libhtml-tagset-perl libhts3t64 libhtscodecs2 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu78 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm21 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libmunge2 libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libpciaccess0 libpipeline1 libpkgconf7 libpmix2t64 libprrte-bin libprrte-dev libprrte3 libpsl5t64 libpsm2-2 librdmacm1t64 librtmp1 libsparsehash-dev libsqlite3-dev libssh2-1t64 libsystemd-shared libtext-markdown-perl libtext-multimarkdown-perl libtool libucc1 libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2-16 libxnvctrl0 libz3-4 libze1 m4 man-db mount ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkgconf pkgconf-bin po-debconf samtools sbuild-build-depends-main-dummy sensible-utils systemd wget zlib1g-dev 0 upgraded, 149 newly installed, 0 to remove and 0 not upgraded. Need to get 154 MB/155 MB of archives. After this operation, 759 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 liblocale-gettext-perl amd64 1.07-8+b1 [15.4 kB] Get:2 copy:/build/abyss-BQNOuM/resolver-v6GwZV/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:3 file:/srv/reprepro perl-5.42/main amd64 libhtml-parser-perl amd64 3.83-1+b4 [100.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 mount amd64 2.41.3-4 [164 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 260.1-1 [2398 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 systemd amd64 260.1-1 [3299 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b1 [338 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b1 [110 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5+b1 [43.8 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.2-2 [242 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.3-4 [98.9 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2 [42.1 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20251016-1 [93.6 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2.1 [28.7 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.16.0-2+b1 [79.3 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2 [33.1 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2 [81.1 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b1 [9784 B] Get:24 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2 [337 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2 [139 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.2p1-6 [1005 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.5-1 [59.9 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 wget amd64 1.25.0-2 [984 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6+b1 [2652 B] Get:30 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-6 [494 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.2-2 [770 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.31 [75.7 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-9 [540 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:41 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.194-4 [183 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.2+dfsg-0.1 [641 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.2-2 [1684 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.31 [932 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16-20260322-1 [886 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libgfortran-15-dev amd64 15.2.0-16 [886 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-16 [12.8 MB] Get:51 http://deb.debian.org/debian unstable/main amd64 gfortran-15 amd64 15.2.0-16 [19.1 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.12.0-2 [62.2 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.12.0-2 [200 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 61.0-2 [64.2 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 61.0-2 [381 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libicu78 amd64 78.3-1 [10.0 MB] Get:58 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 78.3-1 [212 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1+b1 [8646 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-7 [28.3 MB] Get:61 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-7 [767 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libamd-comgr3 amd64 7.0.2+dfsg-3 [13.9 MB] Get:63 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.131-1 [9168 B] Get:64 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.131-1 [39.9 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [24.5 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1+b1 [22.5 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.4.3+dfsg-5 [678 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libamdhip64-6 amd64 6.4.3-5 [9385 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libboost1.90-dev amd64 1.90.0-5+b1 [11.3 MB] Get:70 http://deb.debian.org/debian unstable/main amd64 libboost-exception1.90-dev amd64 1.90.0-5+b1 [222 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.90.0 amd64 1.90.0-5+b1 [355 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.90.0 amd64 1.90.0-5+b1 [327 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 78.3-1 [11.1 MB] Get:74 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.90-dev amd64 1.90.0-5+b1 [343 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.90.0 amd64 1.90.0-5+b1 [326 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.90-dev amd64 1.90.0-5+b1 [364 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libboost-test1.90.0 amd64 1.90.0-5+b1 [465 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libboost-test1.90-dev amd64 1.90.0-5+b1 [534 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.90-dev amd64 1.90.0-5+b1 [378 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libboost-graph-dev amd64 1.90.0.1 [2924 B] Get:81 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libcpptoml-dev all 0.1.1-3 [180 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.21.0-1 [136 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.68.0-2 [79.2 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.21.0-1 [23.5 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3+b1 [60.7 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-2 [244 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.19.0-3 [402 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2+b1 [49.5 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.5-1 [102 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b1 [477 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.6+20251231-1 [106 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.22.1-1 [697 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libbtllib-dev amd64 1.7.5+dfsg-2 [218 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b2 [184 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b2 [134 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b2 [108 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b2 [54.3 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b2 [61.3 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b2 [308 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 61.0-2 [73.0 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1+b1 [716 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libfuse3-4 amd64 3.18.2-1 [103 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.34-2 [111 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.13.0-2 [165 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.19-1+b1 [36.7 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-9 [416 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-9 [168 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.13.0-2 [258 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b4 [52.1 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b1 [20.8 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2 [27.9 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b3 [14.1 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.28.2-2 [795 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.4-1 [43.0 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.13.0-2 [23.5 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 61.0-2 [30.2 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 61.0-2 [44.9 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.12.0-2 [105 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.12.0-2 [220 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 61.0-2 [686 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.18-1 [18.8 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0+really5.0.9-3 [673 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.20.0+ds-4 [938 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.7.0~rc1-1 [329 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.10-1 [2018 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.10-1 [30.3 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 libprrte3 amd64 3.0.13-3 [451 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 libprrte-dev amd64 3.0.13-3 [3654 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-1 [918 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 libprrte-bin amd64 3.0.13-3 [51.9 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.10-1 [154 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.10-1 [1028 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-9+b1 [1112 kB] Get:146 http://deb.debian.org/debian unstable/main amd64 libtext-markdown-perl all 1.000031-5 [31.4 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 libtext-multimarkdown-perl all 1.000035-3 [28.5 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Preconfiguring packages ... Fetched 154 MB in 1s (145 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 23435 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-8+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-8+b1) ... Selecting previously unselected package mount. Preparing to unpack .../mount_2.41.3-4_amd64.deb ... Unpacking mount (2.41.3-4) ... Selecting previously unselected package libsystemd-shared:amd64. Preparing to unpack .../libsystemd-shared_260.1-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (260.1-1) ... Setting up libsystemd-shared:amd64 (260.1-1) ... Selecting previously unselected package systemd. (Reading database ... 23485 files and directories currently installed.) Preparing to unpack .../000-systemd_260.1-1_amd64.deb ... Unpacking systemd (260.1-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.26_all.deb ... 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Setting up libmagic-mgc (1:5.46-5+b1) ... Setting up libcbor0.10:amd64 (0.10.2-2.1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:amd64 (0.2.6+b1) ... Setting up libxml2-16:amd64 (2.15.2+dfsg-0.1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.31) ... Setting up libbrotli1:amd64 (1.2.0-3) ... Setting up libedit2:amd64 (3.1-20251016-1) ... Setting up libpkgconf7:amd64 (2.5.1-4) ... Setting up libmagic1t64:amd64 (1:5.46-5+b1) ... Setting up libpsl5t64:amd64 (0.21.5-1) ... Setting up libnghttp2-14:amd64 (1.68.0-2) ... Setting up libibumad3:amd64 (61.0-2) ... Setting up libdeflate0:amd64 (1.23-2+b1) ... Setting up gettext-base (0.23.2-2) ... Setting up m4 (1.4.21-1) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libibmad5:amd64 (61.0-2) ... Setting up libcom-err2:amd64 (1.47.4-1) ... Setting up file (1:5.46-5+b1) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up libze1:amd64 (1.28.2-2) ... Setting up libelf1t64:amd64 (0.194-4) ... Setting up libkrb5support0:amd64 (1.22.1-2) ... Setting up libicu78:amd64 (78.3-1) ... Setting up autotools-dev (20240727.1) ... Setting up libz3-4:amd64 (4.13.3-1+b1) ... Setting up libmunge2:amd64 (0.5.18-1) ... Setting up libsqlite3-dev:amd64 (3.46.1-9+b1) ... Setting up libx11-data (2:1.8.13-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3+b1) ... Setting up libcpptoml-dev (0.1.1-3) ... Setting up libllvm21:amd64 (1:21.1.8-7) ... Setting up libncurses6:amd64 (6.6+20251231-1) ... Setting up libhwloc15:amd64 (2.13.0-2) ... Setting up autopoint (0.23.2-2) ... Setting up icu-devtools (78.3-1) ... Setting up pkgconf-bin (2.5.1-4) ... Setting up libk5crypto3:amd64 (1.22.1-2) ... Setting up libltdl7:amd64 (2.5.4-9) ... Setting up libgfortran5:amd64 (16-20260322-1) ... Setting up autoconf (2.72-6) ... Setting up libnghttp3-9:amd64 (1.15.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-1) ... Setting up libnuma1:amd64 (2.0.19-1+b1) ... Setting up dwz (0.16-4) ... Setting up mount (2.41.3-4) ... Setting up sensible-utils (0.0.26) ... Setting up ocl-icd-libopencl1:amd64 (2.3.4-1) ... Setting up libuchardet0:amd64 (0.0.8-2+b1) ... Setting up libnl-3-200:amd64 (3.12.0-2) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.10-1) ... Setting up libboost1.90-dev:amd64 (1.90.0-5+b1) ... Setting up libx11-6:amd64 (2:1.8.13-1) ... Setting up libngtcp2-16:amd64 (1.21.0-1) ... Setting up libboost-serialization1.90.0:amd64 (1.90.0-5+b1) ... Setting up libkrb5-3:amd64 (1.22.1-2) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libboost-regex1.90.0:amd64 (1.90.0-5+b1) ... Setting up libclang-common-21-dev:amd64 (1:21.1.8-7) ... Setting up libssh2-1t64:amd64 (1.11.1-2) ... Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1) ... Setting up libfuse3-4:amd64 (3.18.2-1) ... Setting up libfido2-1:amd64 (1.16.0-2+b1) ... Setting up libdrm-common (2.4.131-1) ... Setting up libicu-dev:amd64 (78.3-1) ... Setting up liburi-perl (5.34-2) ... Setting up liblocale-gettext-perl (1.07-8+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.21.0-1) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libboost-serialization1.90-dev:amd64 (1.90.0-5+b1) ... Setting up gettext (0.23.2-2) ... Setting up wget (1.25.0-2) ... Setting up libtool (2.5.4-9) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up libxext6:amd64 (2:1.3.4-1+b4) ... Setting up systemd (260.1-1) ... Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' → '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' → '/usr/lib/systemd/system/systemd-pstore.service'. Created symlink '/etc/systemd/system/autovt@.service' → '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' → '/usr/lib/systemd/system/getty@.service'. Initializing machine ID from random generator. Creating group 'lpadmin' with GID 996. Setting up libgfortran-15-dev:amd64 (15.2.0-16) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.19-1+b1) ... Setting up libnl-route-3-200:amd64 (3.12.0-2) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b3) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (22) ... Setting up libltdl-dev:amd64 (2.5.4-9) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-2) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b2) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libboost-exception1.90-dev:amd64 (1.90.0-5+b1) ... Setting up libdrm2:amd64 (2.4.131-1) ... Setting up libnl-3-dev:amd64 (3.12.0-2) ... Setting up libboost-regex1.90-dev:amd64 (1.90.0-5+b1) ... Setting up groff-base (1.23.0-10) ... Setting up libamd-comgr3:amd64 (7.0.2+dfsg-3) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b4) ... Setting up libhwloc-dev:amd64 (2.13.0-2) ... Setting up libtext-multimarkdown-perl (1.000035-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... Setting up libboost-test1.90-dev:amd64 (1.90.0-5+b1) ... Setting up gfortran-15-x86-64-linux-gnu (15.2.0-16) ... Setting up libibverbs1:amd64 (61.0-2) ... Setting up ibverbs-providers:amd64 (61.0-2) ... Setting up openssh-client (1:10.2p1-6) ... Created symlink '/etc/systemd/user/sockets.target.wants/ssh-agent.socket' → '/usr/lib/systemd/user/ssh-agent.socket'. Setting up po-debconf (1.0.22) ... Setting up libcurl3t64-gnutls:amd64 (8.19.0-3) ... Setting up libhwloc-plugins:amd64 (2.13.0-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'. Setting up libnl-route-3-dev:amd64 (3.12.0-2) ... Setting up libevent-dev (2.1.12-stable-10+b2) ... Setting up libpmix2t64:amd64 (6.0.0+really5.0.9-3) ... Setting up libboost-graph1.90-dev:amd64 (1.90.0-5+b1) ... Setting up libhsa-runtime64-1:amd64 (6.4.3+dfsg-5) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1+b1) ... Setting up librdmacm1t64:amd64 (61.0-2) ... Setting up gfortran-15 (15.2.0-16) ... Setting up libfabric1:amd64 (2.1.0-1.1+b1) ... Setting up libboost-graph-dev:amd64 (1.90.0.1) ... Setting up debhelper (13.31) ... Setting up libibverbs-dev:amd64 (61.0-2) ... Setting up samtools (1.22.1-1) ... Setting up libamdhip64-6:amd64 (6.4.3-5) ... Setting up libprrte3:amd64 (3.0.13-3) ... Setting up libprrte-dev:amd64 (3.0.13-3) ... Setting up libprrte-bin (3.0.13-3) ... Setting up libucx0:amd64 (1.20.0+ds-4) ... Setting up libbtllib-dev (1.7.5+dfsg-2) ... Setting up libucc1:amd64 (1.7.0~rc1-1) ... Setting up libopenmpi40:amd64 (5.0.10-1) ... Setting up openmpi-bin (5.0.10-1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) does not exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev (5.0.10-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-14) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 29 Mar 2026 04:02:26 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sun, 29 Mar 2026 04:02:26 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.18.5+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.18.5-1 (2026-01-16) amd64 (x86_64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-14_14.3.0-14 g++-15_15.2.0-16 gcc-14_14.3.0-14 gcc-15_15.2.0-16 libc6-dev_2.42-14 libstdc++-14-dev_14.3.0-14 libstdc++-15-dev_15.2.0-16 libstdc++6_16-20260322-1 linux-libc-dev_6.19.10-1 Package versions: adduser_3.155 apt_3.1.16 architecture-properties_0.2.6+b1 autoconf_2.72-6 automake_1:1.18.1-4 autopoint_0.23.2-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-2 binutils_2.46-3 binutils-common_2.46-3 binutils-gold_2.44-3 binutils-gold-x86-64-linux-gnu_2.44-3 binutils-x86-64-linux-gnu_2.46-3 bsdextrautils_2.41.3-4 bsdutils_1:2.41.3-4 build-essential_12.12 bzip2_1.0.8-6+b1 coreutils_9.10-1 cpp_4:15.2.0-5 cpp-14_14.3.0-14 cpp-14-x86-64-linux-gnu_14.3.0-14 cpp-15_15.2.0-16 cpp-15-x86-64-linux-gnu_15.2.0-16 cpp-x86-64-linux-gnu_4:15.2.0-5 dash_0.5.12-12 debconf_1.5.92 debhelper_13.31 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dirmngr_2.4.9-4 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.46-5+b1 findutils_4.10.0-3 g++_4:15.2.0-5 g++-14_14.3.0-14 g++-14-x86-64-linux-gnu_14.3.0-14 g++-15_15.2.0-16 g++-15-x86-64-linux-gnu_15.2.0-16 g++-x86-64-linux-gnu_4:15.2.0-5 gcc_4:15.2.0-5 gcc-14_14.3.0-14 gcc-14-base_14.3.0-14 gcc-14-x86-64-linux-gnu_14.3.0-14 gcc-15_15.2.0-16 gcc-15-base_15.2.0-16 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perl-modules-5.42_5.42.0-3 pinentry-curses_1.3.2-4 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.3-1 samtools_1.22.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.26 sqv_1.3.0-5 systemd_260.1-1 sysvinit-utils_3.15-6 tar_1.35+dfsg-4 util-linux_2.41.3-4 wget_1.25.0-2 xz-utils_5.8.2-2 zlib1g_1:1.3.dfsg+really1.3.2-1 zlib1g-dev_1:1.3.dfsg+really1.3.2-1 +------------------------------------------------------------------------------+ | Build Sun, 29 Mar 2026 04:02:26 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: abyss Binary: abyss Architecture: any Version: 2.3.10-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://github.com/bcgsc/abyss Standards-Version: 4.7.3 Vcs-Browser: https://salsa.debian.org/med-team/abyss Vcs-Git: https://salsa.debian.org/med-team/abyss.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), architecture-is-64-bit, libboost-graph-dev, libbtllib-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl , libsqlite3-dev, pkgconf, help2man, debhelper Package-List: abyss deb science optional arch=any Checksums-Sha1: 2179eef8d6120588e46efb7397cc7ba3cfca5c26 933928 abyss_2.3.10.orig.tar.xz a210025740769cf4cdff02033b2d7bded14b1e3d 1498988 abyss_2.3.10-2.debian.tar.xz Checksums-Sha256: c8461eb017edfbd83c2aac9910da438df2d79660d2e87ab289f2de7a0d620a4c 933928 abyss_2.3.10.orig.tar.xz 9aa08c1d204890c7e61835779d326d315adcb8eaf48129623a4d4d06a9838002 1498988 abyss_2.3.10-2.debian.tar.xz Files: b13b49e294474086d2e1395f5689843b 933928 abyss_2.3.10.orig.tar.xz 33ef8a28a8bad85624038751b9330316 1498988 abyss_2.3.10-2.debian.tar.xz Dgit: f8001fd2cf010752471aa52309cef4f9486ab068 debian archive/debian/2.3.10-2 https://git.dgit.debian.org/abyss -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmnIPUEUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdq1zw//cmZIB++A0A/kXPpFKKLZU1biybcf EWRPxti/gbcqMwqGF7ajI2+EXXq5I8mtzJz4dYK9i2UiryjdD3eTjX1Zt+0a7u1G ASk/GEEwW22EL3FYV5S5tM5Elr+cH/mEztIzmB4s/4/k9hFdxEHzu68TbBeKxcIX C0b4BRxGUYpdwAjHcWJuCUOS3UGWJ8cBUAFYmrIEQnokSADeSkRzF7UQfoYx/FA9 yjg5fDrSoP8CFp7JdbTNuMwyW06640h75ab7n5RRBWZZA+60g9NclO1r88/51luQ hCAi+fXsT1tgZCKHBzRce8BCufQddh/cy6SXedlfkBcw3S3iCM2TMt05iKo8kx2l dgT/ySJsqox4wh0EtS5oUyzN/tlysIBRRUb38ldjBl48vBo8PhD0PYgYDdT2hmjX IhN1f0ctwNdoOUIxoJcK5zuHXW+KFFdqRNgZ54RSJSsORlxPXNbx7PQcR7b6gpJl 82rHRCtHzUo4eXbON2CBV71ae/6QfD7tbD9OW363cE/v1CXxfqs7ErFIINubm2HZ WjtbcNyyCrd5xWwcd1jRiu5b39FfVDXsfykNgM3538W8jnDINGiEPj9R2G/Y/CFV 7R3ZMU49nHsQJoGW7hz1dnTIzGLZ0zxF72vm9/5j8dxbZWiRlkkA37sksy64WBdT LcMEUu1U5cKtiFc= =C6a6 -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./abyss_2.3.10-2.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./abyss_2.3.10-2.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting abyss in /build/abyss-BQNOuM/abyss-2.3.10 dpkg-source: info: unpacking abyss_2.3.10.orig.tar.xz dpkg-source: info: unpacking abyss_2.3.10-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying fix-privacy-breach.patch dpkg-source: info: applying gcc-16.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Sun, 29 Mar 2026 04:02:27 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network abyss_2.3.10-2 perl-5.42-throwaway amd64 --------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network abyss_2.3.10-2 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en 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=/build/abyss-BQNOuM/abyss-2.3.10 SCHROOT_ALIAS_NAME=perl-5.42-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-95cfaf21-44ec-4c2b-bbb5-6a6f2ac0454c SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.3.10-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building abyss using existing ../abyss_2.3.10.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building abyss in ../abyss_2.3.10-2.debian.tar.xz dpkg-source: info: building abyss in ../abyss_2.3.10-2.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing configure.ac:25: installing './ar-lib' configure.ac:16: installing './compile' configure.ac:80: installing './config.guess' configure.ac:80: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' autoreconf: Leaving directory '.' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' dh_auto_configure -- \ --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether g++ supports C++11 features with -std=c++11... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking whether UID '1002' is supported by ustar format... yes checking whether GID '110' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking dependency style of g++ -std=c++11... none checking for gawk... (cached) mawk checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=c++11 accepts -g... (cached) yes checking for g++ -std=c++11 option to enable C++11 features... (cached) none needed checking for ranlib... ranlib checking for ghc... no checking for pandoc... no checking for ar... ar checking the archiver (ar) interface... ar checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for vfork.h... no checking for dlfcn.h... yes checking for fcntl.h... yes checking for float.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for sys/param.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for std::hash... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... yes checking for dup2... yes checking for gethostname... yes checking for getopt_long... yes checking for getpagesize... yes checking for memset... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking for fork... yes checking for vfork... yes checking for vprintf... yes checking for working fork... yes checking for working vfork... (cached) yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for GNU libc compatible realloc... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether HOST_NAME_MAX is declared... yes checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking for functional... yes checking for tr1/functional... yes checking for boost/functional/hash.hpp... yes checking for boost/property_map/property_map.hpp... yes checking for google/sparse_hash_map... yes checking for unordered_map... yes checking for tr1/unordered_map... yes checking for unordered_set... yes checking for tr1/unordered_set... yes checking for boost/unordered_set.hpp... yes checking for btllib/bloom_filter.hpp... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for g++ -std=c++11 option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating vendor/gtest-1.7.0/Makefile config.status: creating RResolver/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating vendor/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' dh_auto_build make -j2 make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' make all-recursive make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' Making all in bin make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/bin' Making all in doc make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/doc' Making all in Common make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc rm -f libcommon.a ar cr libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o ranlib libcommon.a make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Common' Making all in Graph make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Graph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc In file included from GraphIO.h:8, from todot.cc:9: DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ todot.cc:186:14: required from here 186 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ todot.cc:191:14: required from here 191 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L. -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Graph' Making all in DataLayer make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc rm -f libdatalayer.a ar cr libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ranlib libdatalayer.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm rm -f libdb.a ar cr libdb.a libdb_a-DB.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o ranlib libdb.a make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc rm -f libfmindex.a ar cr libfmindex.a libfmindex_a-bit_array.o ranlib libfmindex.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/FMIndex' Making all in Assembly make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc rm -f libassembly.a ar cr libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o ranlib libassembly.a make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Assembly' Making all in dialign make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o alig.o alig.c alig.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o assemble.o assemble.c assemble.c:40:20: warning: inline function ‘align_diag’ declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never defined 37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); | ^~~~~~~~ assemble.c:25:39: warning: inline function ‘find_diags_guided’ declared but never defined 25 | extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, | ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o diag.o diag.c diag.c:1456:17: warning: ‘real_calc_weight’ is static but used in inline function ‘find_diags_dyn’ which is not static 1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); | ^~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o io.o io.c io.c: In function ‘read_scr_matrix’: io.c:270:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 270 | fscanf( fp, "%i", &is); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:282:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 282 | fscanf(fp, "%s\n", rline); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘read_diag_prob_dist’: io.c:371:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o translate.o translate.c rm -f libdialign.a ar cr libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ranlib libdialign.a gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/dialign' Making all in Align make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Align' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc rm -f libalign.a ar cr libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o ranlib libalign.a g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Align' Making all in ABYSS make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/ABYSS' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/ABYSS' Making all in Parallel make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Parallel' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Parallel' Making all in Bloom make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Bloom' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/BloomDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Konnector' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Konnector' Making all in Consensus make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Consensus' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Consensus' Making all in DAssembler make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DAssembler' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DistanceEst' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/KAligner' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/KAligner' Making all in Layout make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Layout' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc In file included from ../Graph/GraphIO.h:8, from layout.cc:8: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ layout.cc:314:12: required from here 314 | write_dot(out, g); | ~~~~~~~~~^~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/LogKmerCount' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/LogKmerCount' Making all in Map make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Map' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc In file included from ../Graph/GraphIO.h:8, from overlap.cc:23: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ overlap.cc:502:13: required from here 502 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Map' Making all in MergePaths make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/MergePaths' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp In file included from ../Graph/GraphIO.h:8, from MergeContigs.cpp:13: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ MergeContigs.cpp:428:13: required from here 428 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm In file included from ../Graph/GraphIO.h:8, from PathConsensus.cpp:16: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PathConsensus.cpp:999:14: required from here 999 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/MergePaths' Making all in Overlap make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Overlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp Overlap.cpp: In function ‘int main(int, char**)’: Overlap.cpp:513:40: warning: possibly dangling reference to a temporary [-Wdangling-reference] 513 | const Overlap& ep = get(edge_bundle, scaffoldGraph, e); | ^~ Overlap.cpp:513:48: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 513 | const Overlap& ep = get(edge_bundle, scaffoldGraph, e); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../Graph/GraphIO.h:8, from Overlap.cpp:16: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Overlap; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ Overlap.cpp:481:35: required from here 481 | cout << dot_writer(scaffoldGraph); | ^ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Overlap.cpp:587:14: required from here 587 | write_graph(fout, graph, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PairedDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o KmerPair.o KmerPair.cc rm -f libpaireddbg.a ar cr libpaireddbg.a KmerPair.o ranlib libpaireddbg.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/ParseAligns' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PathOverlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp In file included from ../Graph/GraphIO.h:8, from PathOverlap.cpp:10: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PathOverlap.cpp:709:14: required from here 709 | write_graph(out, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PopBubbles' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp In file included from ../Graph/GraphIO.h:8, from PopBubbles.cpp:16: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PopBubbles.cpp:723:14: required from here 723 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Scaffold' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc In file included from ../Graph/GraphIO.h:8, from scaffold.cc:13: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ scaffold.cc:824:13: required from here 824 | write_dot(out, g); | ~~~~~~~~~^~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp In file included from ../Graph/GraphIO.h:8, from longseqdist.cpp:9: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ longseqdist.cpp:208:11: required from here 208 | write_dot(cout, g); | ~~~~~~~~~^~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/SimpleGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/kmerprint' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/FilterGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc In file included from ../Graph/GraphIO.h:8, from FilterGraph.cc:15: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ FilterGraph.cc:825:14: required from here 825 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/GapFiller' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/GapFiller' Making all in Sealer make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Sealer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Sealer' Making all in RResolver make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/RResolver' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_rresolver_short-RResolverShort.o `test -f 'RResolverShort.cpp' || echo './'`RResolverShort.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp In file included from ../Graph/GraphIO.h:8, from Contigs.h:17, from Contigs.cpp:1: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Contigs.cpp:140:13: required from here 140 | write_graph(fout, g_contigGraph, program, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-RAlgorithmsShort.o `test -f 'RAlgorithmsShort.cpp' || echo './'`RAlgorithmsShort.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-BloomFilters.o `test -f 'BloomFilters.cpp' || echo './'`BloomFilters.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp In file included from ../Graph/GraphIO.h:8, from Contigs.h:17, from Contigs.cpp:1: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Contigs.cpp:140:13: required from here 140 | write_graph(fout, g_contigGraph, program, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-SequenceTree.o `test -f 'SequenceTree.cpp' || echo './'`SequenceTree.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-RUtils.o `test -f 'RUtils.cpp' || echo './'`RUtils.cpp rm -f libralgorithmsshort.a ar cr libralgorithmsshort.a libralgorithmsshort_a-RAlgorithmsShort.o libralgorithmsshort_a-BloomFilters.o libralgorithmsshort_a-Contigs.o libralgorithmsshort_a-SequenceTree.o libralgorithmsshort_a-RUtils.o ../DataLayer/abyss_fac-fac.o ../DataLayer/abyss_tofastq-abyss-tofastq.o ../DataLayer/libdatalayer_a-FastaReader.o ../DataLayer/libdatalayer_a-FastaWriter.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o ranlib libralgorithmsshort.a g++ -std=c++11 -Wall -Wextra -Werror -Wno-deprecated-declarations -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -pthread -o abyss-rresolver-short abyss_rresolver_short-RResolverShort.o abyss_rresolver_short-Contigs.o ../DataLayer/libdatalayer.a ../Common/libcommon.a libralgorithmsshort.a -lbtllib -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/RResolver' Making all in AdjList make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/AdjList' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp In file included from ../Graph/GraphIO.h:8, from AdjList.cpp:15: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ AdjList.cpp:401:13: required from here 401 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/AdjList' Making all in vendor make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' markdown README.md > README.html make[1]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' dh_auto_test make -j2 check TESTSUITEFLAGS="-j2 --verbose" VERBOSE=1 make[1]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' Making check in bin make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/bin' Making check in doc make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/doc' Making check in Common make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Common' Making check in Graph make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Graph' Making check in DataLayer make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DataLayer' Making check in DataBase make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DataBase' Making check in FMIndex make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/FMIndex' Making check in Assembly make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Assembly' Making check in dialign make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/dialign' Making check in Align make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Align' Making check in ABYSS make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/ABYSS' Making check in Parallel make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Parallel' Making check in Bloom make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Bloom' Making check in BloomDBG make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/BloomDBG' Making check in Konnector make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Konnector' Making check in Consensus make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Consensus' Making check in DAssembler make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/KAligner' Making check in Layout make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/LogKmerCount' Making check in Map make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Map' Making check in MergePaths make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/MergePaths' Making check in Overlap make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Overlap' Making check in PairedDBG make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/GapFiller' Making check in Sealer make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Sealer' Making check in RResolver make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/RResolver' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/RResolver' Making check in AdjList make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/AdjList' Making check in vendor make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor' Making check in vendor/gtest-1.7.0 make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor/gtest-1.7.0' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc rm -f libgtest.a ar cr libgtest.a src/libgtest_a-gtest-all.o ranlib libgtest.a rm -f libgtest_main.a ar cr libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o ranlib libgtest_main.a make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor/gtest-1.7.0' make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam common_sam_ssq BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_CountingBloomFilter BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/HistogramTest.o Common/HistogramTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/KmerTest.o Common/KmerTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/Sequence.o Common/Sequence.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/SAM.o Common/SAM.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -DSAM_SEQ_QUAL -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Common/common_sam_ssq-SAM.o `test -f 'Common/SAM.cc' || echo './'`Common/SAM.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Konnector/DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o DBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o PairedDBG/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o PairedDBG/Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o PairedDBG/BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o `test -f 'BloomDBG/CountingBloomFilterTest.cpp' || echo './'`BloomDBG/CountingBloomFilterTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-BQNOuM/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-BQNOuM/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam_ssq Common/common_sam_ssq-SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-BQNOuM/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make check-TESTS make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' PASS: common_stringutil PASS: common_histogram PASS: common_bitutil PASS: common_kmer PASS: common_sequence PASS: common_KmerIterator PASS: common_sam PASS: common_sam_ssq PASS: BloomFilter PASS: Konnector_DBGBloom PASS: Konnector_DBGBloomAlgorithms PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_ExtendPath PASS: graph_DotIO PASS: Konnector_konnector PASS: graph_UndirectedGraph PASS: PairedDBG_LoadAlgorithm PASS: DBG_LoadAlgorithm PASS: PairedDBG_Dinuc PASS: PairedDBG_KmerPair PASS: PairedDBG_BranchRecord PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer ============================================================================ Testsuite summary for ABySS 2.3.10 ============================================================================ # TOTAL: 34 # PASS: 34 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' make[1]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' dh_auto_install --destdir=debian/tmp make -j2 install DESTDIR=/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' Making install in bin make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/bin' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/bin' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/bin' Making install in doc make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/doc' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/doc' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/doc' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/doc' Making install in Common make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Common' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Common' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Common' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Common' Making install in Graph make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Graph' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Graph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Graph' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Graph' Making install in DataLayer make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DataLayer' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DataLayer' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DataLayer' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DataLayer' Making install in DataBase make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DataBase' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DataBase' /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DataBase' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DataBase' Making install in FMIndex make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/FMIndex' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/FMIndex' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/FMIndex' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/FMIndex' Making install in Assembly make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Assembly' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Assembly' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Assembly' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Assembly' Making install in dialign make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/dialign' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/dialign' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/dialign' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/dialign' Making install in Align make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Align' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Align' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Align' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Align' Making install in ABYSS make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/ABYSS' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/ABYSS' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/ABYSS' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Parallel' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Parallel' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Parallel' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Parallel' Making install in Bloom make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Bloom' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Bloom' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Bloom' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/BloomDBG' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/BloomDBG' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Konnector' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Konnector' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Konnector' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Consensus' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Consensus' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Consensus' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DAssembler' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DAssembler' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DistanceEst' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DistanceEst' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/KAligner' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/KAligner' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/KAligner' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/KAligner' Making install in Layout make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Layout' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Layout' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Layout' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/LogKmerCount' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/LogKmerCount' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Map' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Map' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Map' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Map' Making install in MergePaths make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/MergePaths' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/MergePaths' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/MergePaths' Making install in Overlap make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Overlap' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Overlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Overlap' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PairedDBG' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PairedDBG' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/ParseAligns' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/ParseAligns' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PathOverlap' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PathOverlap' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PopBubbles' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PopBubbles' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Scaffold' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Scaffold' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/SimpleGraph' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/SimpleGraph' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/kmerprint' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/kmerprint' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/kmerprint' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/FilterGraph' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/FilterGraph' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/GapFiller' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/GapFiller' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/GapFiller' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/GapFiller' Making install in Sealer make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Sealer' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Sealer' /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Sealer' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Sealer' Making install in RResolver make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/RResolver' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/RResolver' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-rresolver-short '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/RResolver' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/RResolver' Making install in AdjList make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/AdjList' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/AdjList' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/AdjList' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/AdjList' Making install in vendor make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor/gtest-1.7.0' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor/gtest-1.7.0' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/vendor/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10/Unittest' make[3]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' make[4]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/abyss-BQNOuM/abyss-2.3.10/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' make[3]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' make[2]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' mkdir -p debian/tmp/usr/share/man/man1 PATH=debian/tmp/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ -n "Estimate distances between contigs using paired-end alignments." \ DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1 PATH=debian/tmp/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \ > debian/tmp/usr/share/man/man1/abyss-fixmate.1 make[1]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' debian/rules override_dh_install make[1]: Entering directory '/build/abyss-BQNOuM/abyss-2.3.10' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/abyss-BQNOuM/abyss-2.3.10' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'abyss' in '../abyss_2.3.10-2_amd64.deb'. dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.10-2_amd64.deb'. dpkg-genbuildinfo -O../abyss_2.3.10-2_amd64.buildinfo dpkg-genchanges -O../abyss_2.3.10-2_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2026-03-29T04:09:36Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 29 Mar 2026 04:09:36 +0000 | +------------------------------------------------------------------------------+ abyss_2.3.10-2_amd64.changes: ----------------------------- Format: 1.8 Date: Sat, 28 Mar 2026 21:29:14 +0100 Source: abyss Binary: abyss abyss-dbgsym Architecture: source amd64 Version: 2.3.10-2 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: abyss - de novo, parallel, sequence assembler for short reads Closes: 1132058 Changes: abyss (2.3.10-2) unstable; urgency=medium . [ Michael R. Crusoe ] * 'btllib' is no longer included in the upstream sources, so the sources don't need to be repacked. . [ Andreas Tille ] * Replace pkg-config with pkgconf in Build-Depends . [ Étienne Mollier ] * gcc-16.patch: new: fix ftbfs with Gcc 16. (Closes: #1132058) * d/watch: convert to Github uscan template v5. * d/control: drop redundant Priority: optional. * d/control: drop redundant Rules-Requires-Root: no. * d/control: declare compliance to standards version 4.7.3. * abyss-pe.patch: fix a typo caught by lintian in description. * d/copyright: remove the old fsf mail address. Checksums-Sha1: bdc031d55cff20e2445c5c7b4022107d555a4b1c 1286 abyss_2.3.10-2.dsc e2a33c64e535134617513cbd2f49f055ae057beb 1498988 abyss_2.3.10-2.debian.tar.xz c63925709011da8b74f94d598c238c7abb08700e 30413612 abyss-dbgsym_2.3.10-2_amd64.deb 6c755fd7f354b1fbe491a4f57329b35996389703 9604 abyss_2.3.10-2_amd64.buildinfo a79b97915b2ceab9cabfa812928d065cec44d519 3348676 abyss_2.3.10-2_amd64.deb Checksums-Sha256: 6e9daf29acb7efdd50a04ef0a12a076fee37db839816297fc579ee79ee7994e9 1286 abyss_2.3.10-2.dsc e1d54fdfbc5706edf1ba4f35105d99edf551ad922b7b82a629abbff7f752cdb6 1498988 abyss_2.3.10-2.debian.tar.xz 698a051de33ef306e836112f357066364836bc3472686af7455153181758b8a4 30413612 abyss-dbgsym_2.3.10-2_amd64.deb 0b6f3b98d35f05fcb7fadb5558a7d23baea455476d03bbed4fde32cde615a2af 9604 abyss_2.3.10-2_amd64.buildinfo 97545a6b07d36959cbd4dc7f8050392d3ee77fd8f676a9e19b8ae5d438eb14ce 3348676 abyss_2.3.10-2_amd64.deb Files: 2db503bc16fe9ace6b3593d73a13d04e 1286 science optional abyss_2.3.10-2.dsc 3a03cf077a37dc461d8498249f86466b 1498988 science optional abyss_2.3.10-2.debian.tar.xz a5d5e0310f3369e1a66a049cfcb84b44 30413612 debug optional abyss-dbgsym_2.3.10-2_amd64.deb 2ba857493b3599aaa823328dccc93fcf 9604 science optional abyss_2.3.10-2_amd64.buildinfo 5c9fd574d58e74e8ef1d4a3d9f54b930 3348676 science optional abyss_2.3.10-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 29 Mar 2026 04:09:36 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: abyss Binary: abyss abyss-dbgsym Architecture: amd64 source Version: 2.3.10-2 Checksums-Md5: 2db503bc16fe9ace6b3593d73a13d04e 1286 abyss_2.3.10-2.dsc a5d5e0310f3369e1a66a049cfcb84b44 30413612 abyss-dbgsym_2.3.10-2_amd64.deb 5c9fd574d58e74e8ef1d4a3d9f54b930 3348676 abyss_2.3.10-2_amd64.deb Checksums-Sha1: bdc031d55cff20e2445c5c7b4022107d555a4b1c 1286 abyss_2.3.10-2.dsc c63925709011da8b74f94d598c238c7abb08700e 30413612 abyss-dbgsym_2.3.10-2_amd64.deb a79b97915b2ceab9cabfa812928d065cec44d519 3348676 abyss_2.3.10-2_amd64.deb Checksums-Sha256: 6e9daf29acb7efdd50a04ef0a12a076fee37db839816297fc579ee79ee7994e9 1286 abyss_2.3.10-2.dsc 698a051de33ef306e836112f357066364836bc3472686af7455153181758b8a4 30413612 abyss-dbgsym_2.3.10-2_amd64.deb 97545a6b07d36959cbd4dc7f8050392d3ee77fd8f676a9e19b8ae5d438eb14ce 3348676 abyss_2.3.10-2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 29 Mar 2026 04:09:35 +0000 Build-Path: /build/abyss-BQNOuM/abyss-2.3.10 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.155), architecture-properties (= 0.2.6+b1), autoconf (= 2.72-6), automake (= 1:1.18.1-4), autopoint (= 0.23.2-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-2), binutils (= 2.46-3), binutils-common (= 2.46-3), binutils-x86-64-linux-gnu (= 2.46-3), bsdextrautils (= 2.41.3-4), build-essential (= 12.12), bzip2 (= 1.0.8-6+b1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5), cpp-14 (= 14.3.0-14), cpp-14-x86-64-linux-gnu (= 14.3.0-14), cpp-15 (= 15.2.0-16), cpp-15-x86-64-linux-gnu (= 15.2.0-16), cpp-x86-64-linux-gnu (= 4:15.2.0-5), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.31), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.46-5+b1), findutils (= 4.10.0-3), g++ (= 4:15.2.0-5), g++-15 (= 15.2.0-16), g++-15-x86-64-linux-gnu (= 15.2.0-16), g++-x86-64-linux-gnu (= 4:15.2.0-5), gcc (= 4:15.2.0-5), gcc-14 (= 14.3.0-14), gcc-14-base (= 14.3.0-14), gcc-14-x86-64-linux-gnu (= 14.3.0-14), gcc-15 (= 15.2.0-16), gcc-15-base (= 15.2.0-16), gcc-15-x86-64-linux-gnu (= 15.2.0-16), gcc-16-base (= 16-20260322-1), gcc-x86-64-linux-gnu (= 4:15.2.0-5), gettext (= 0.23.2-2), gettext-base (= 0.23.2-2), gfortran-15 (= 15.2.0-16), gfortran-15-x86-64-linux-gnu (= 15.2.0-16), grep (= 3.12-1), groff-base (= 1.23.0-10), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), ibverbs-providers (= 61.0-2), icu-devtools (= 78.3-1), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libamd-comgr3 (= 7.0.2+dfsg-3), libamdhip64-6 (= 6.4.3-5), libarchive-zip-perl (= 1.68-1), libasan8 (= 16-20260322-1), libatomic1 (= 16-20260322-1), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46-3), libblkid1 (= 2.41.3-4), libboost-exception1.90-dev (= 1.90.0-5+b1), libboost-graph-dev (= 1.90.0.1), libboost-graph1.90-dev (= 1.90.0-5+b1), libboost-graph1.90.0 (= 1.90.0-5+b1), libboost-regex1.90-dev (= 1.90.0-5+b1), libboost-regex1.90.0 (= 1.90.0-5+b1), libboost-serialization1.90-dev (= 1.90.0-5+b1), libboost-serialization1.90.0 (= 1.90.0-5+b1), libboost-test1.90-dev (= 1.90.0-5+b1), libboost-test1.90.0 (= 1.90.0-5+b1), libboost1.90-dev (= 1.90.0-5+b1), libbrotli1 (= 1.2.0-3), libbsd0 (= 0.12.2-2+b1), libbtllib-dev (= 1.7.5+dfsg-2), libbz2-1.0 (= 1.0.8-6+b1), libc-bin (= 2.42-14), libc-dev-bin (= 2.42-14), libc-gconv-modules-extra (= 2.42-14), libc6 (= 2.42-14), libc6-dev (= 2.42-14), libcap-ng0 (= 0.9.1-1), libcbor0.10 (= 0.10.2-2.1), libcc1-0 (= 16-20260322-1), libclang-common-21-dev (= 1:21.1.8-7), libcom-err2 (= 1.47.4-1), libcpptoml-dev (= 0.1.1-3), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.46-3), libctf0 (= 2.46-3), libcurl3t64-gnutls (= 8.19.0-3), libdb5.3t64 (= 5.3.28+dfsg2-11), libdebconfclient0 (= 0.282+b2), libdebhelper-perl (= 13.31), libdeflate0 (= 1.23-2+b1), libdpkg-perl (= 1.23.7), libdrm-amdgpu1 (= 2.4.131-1), libdrm-common (= 2.4.131-1), libdrm2 (= 2.4.131-1), libedit2 (= 3.1-20251016-1), libelf1t64 (= 0.194-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-core-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-dev (= 2.1.12-stable-10+b2), libevent-extra-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-openssl-2.1-7t64 (= 2.1.12-stable-10+b2), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10+b2), libfabric1 (= 2.1.0-1.1+b1), libffi8 (= 3.5.2-4), libfido2-1 (= 1.16.0-2+b1), libfile-stripnondeterminism-perl (= 1.15.0-1), libfuse3-4 (= 3.18.2-1), libgcc-14-dev (= 14.3.0-14), libgcc-15-dev (= 15.2.0-16), libgcc-s1 (= 16-20260322-1), libgdbm-compat4t64 (= 1.26-1+b1), libgdbm6t64 (= 1.26-1+b1), libgfortran-15-dev (= 15.2.0-16), libgfortran5 (= 16-20260322-1), libgmp10 (= 2:6.3.0+dfsg-5+b1), libgnutls30t64 (= 3.8.12-3), libgomp1 (= 16-20260322-1), libgprofng0 (= 2.46-3), libgssapi-krb5-2 (= 1.22.1-2), libhogweed6t64 (= 3.10.2-1), libhsa-runtime64-1 (= 6.4.3+dfsg-5), libhtml-parser-perl (= 3.83-1+b4), libhtml-tagset-perl (= 3.24-1), libhts3t64 (= 1.22.1+ds2-1+b1), libhtscodecs2 (= 1.6.5-1), libhwasan0 (= 16-20260322-1), libhwloc-dev (= 2.13.0-2), libhwloc-plugins (= 2.13.0-2), libhwloc15 (= 2.13.0-2), libibmad5 (= 61.0-2), libibumad3 (= 61.0-2), libibverbs-dev (= 61.0-2), libibverbs1 (= 61.0-2), libicu-dev (= 78.3-1), libicu78 (= 78.3-1), libidn2-0 (= 2.3.8-4+b1), libisl23 (= 0.27-2), libitm1 (= 16-20260322-1), libjansson4 (= 2.14-2+b4), libjs-jquery (= 3.7.1+dfsg+~3.5.33-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libk5crypto3 (= 1.22.1-2), libkeyutils1 (= 1.6.3-6+b1), libkrb5-3 (= 1.22.1-2), libkrb5support0 (= 1.22.1-2), libldap2 (= 2.6.10+dfsg-1+b2), libllvm21 (= 1:21.1.8-7), liblocale-gettext-perl (= 1.07-8+b1), liblsan0 (= 16-20260322-1), libltdl-dev (= 2.5.4-9), libltdl7 (= 2.5.4-9), liblzma5 (= 5.8.2-2), libmagic-mgc (= 1:5.46-5+b1), libmagic1t64 (= 1:5.46-5+b1), libmd0 (= 1.1.0-2+b2), libmount1 (= 2.41.3-4), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libmunge2 (= 0.5.18-1), libncurses6 (= 6.6+20251231-1), libnettle8t64 (= 3.10.2-1), libnghttp2-14 (= 1.68.0-2), libnghttp3-9 (= 1.15.0-1), libngtcp2-16 (= 1.21.0-1), libngtcp2-crypto-gnutls8 (= 1.21.0-1), libnl-3-200 (= 3.12.0-2), libnl-3-dev (= 3.12.0-2), libnl-route-3-200 (= 3.12.0-2), libnl-route-3-dev (= 3.12.0-2), libnuma-dev (= 2.0.19-1+b1), libnuma1 (= 2.0.19-1+b1), libopenmpi-dev (= 5.0.10-1), libopenmpi40 (= 5.0.10-1), libp11-kit0 (= 0.26.2-2), libpam-modules (= 1.7.0-5+b1), libpam-modules-bin (= 1.7.0-5+b1), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5+b1), libpciaccess0 (= 0.17-3+b4), libpcre2-8-0 (= 10.46-1+b1), libperl5.42 (= 5.42.0-3), libpipeline1 (= 1.5.8-2), libpkgconf7 (= 2.5.1-4), libpmix2t64 (= 6.0.0+really5.0.9-3), libprrte-bin (= 3.0.13-3), libprrte-dev (= 3.0.13-3), libprrte3 (= 3.0.13-3), libpsl5t64 (= 0.21.5-1), libpsm2-2 (= 11.2.185-2.1), libquadmath0 (= 16-20260322-1), librdmacm1t64 (= 61.0-2), librtmp1 (= 2.4+20151223.gitfa8646d.1-3+b1), libsasl2-2 (= 2.1.28+dfsg1-10), libsasl2-modules-db (= 2.1.28+dfsg1-10), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.9-4+b1), libsemanage-common (= 3.9-1), libsemanage2 (= 3.9-1+b1), libsepol2 (= 3.9-2), libsframe3 (= 2.46-3), libsmartcols1 (= 2.41.3-4), libsparsehash-dev (= 2.0.3-2), libsqlite3-0 (= 3.46.1-9+b1), libsqlite3-dev (= 3.46.1-9+b1), libssh2-1t64 (= 1.11.1-2), libssl3t64 (= 3.6.1-3), libstdc++-15-dev (= 15.2.0-16), libstdc++6 (= 16-20260322-1), libsystemd-shared (= 260.1-1), libsystemd0 (= 260.1-1), libtasn1-6 (= 4.21.0-2), libtext-markdown-perl (= 1.000031-5), libtext-multimarkdown-perl (= 1.000035-3), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-9), libtsan2 (= 16-20260322-1), libubsan1 (= 16-20260322-1), libucc1 (= 1.7.0~rc1-1), libuchardet0 (= 0.0.8-2+b1), libucx0 (= 1.20.0+ds-4), libudev1 (= 260.1-1), libunistring5 (= 1.4.2-1), liburi-perl (= 5.34-2), libuuid1 (= 2.41.3-4), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b1), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2), libxext6 (= 2:1.3.4-1+b4), libxml2-16 (= 2.15.2+dfsg-0.1), libxnvctrl0 (= 535.171.04-1+b3), libz3-4 (= 4.13.3-1+b1), libze1 (= 1.28.2-2), libzstd1 (= 1.5.7+dfsg-3+b1), linux-libc-dev (= 6.19.10-1), login.defs (= 1:4.19.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), mount (= 2.41.3-4), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), ocl-icd-libopencl1 (= 2.3.4-1), openmpi-bin (= 5.0.10-1), openmpi-common (= 5.0.10-1), openssh-client (= 1:10.2p1-6), openssl-provider-legacy (= 3.6.1-3), passwd (= 1:4.19.3-1), patch (= 2.8-2), perl (= 5.42.0-3), perl-base (= 5.42.0-3), perl-modules-5.42 (= 5.42.0-3), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), rpcsvc-proto (= 1.4.3-1), samtools (= 1.22.1-1), sed (= 4.9-2), sensible-utils (= 0.0.26), systemd (= 260.1-1), sysvinit-utils (= 3.15-6), tar (= 1.35+dfsg-4), util-linux (= 2.41.3-4), wget (= 1.25.0-2), xz-utils (= 5.8.2-2), zlib1g (= 1:1.3.dfsg+really1.3.2-1), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1774729754" +------------------------------------------------------------------------------+ | Package contents Sun, 29 Mar 2026 04:09:36 +0000 | +------------------------------------------------------------------------------+ abyss-dbgsym_2.3.10-2_amd64.deb ------------------------------- new Debian package, version 2.0. size 30413612 bytes: control archive=2532 bytes. 2088 bytes, 12 lines control 4640 bytes, 44 lines md5sums Package: abyss-dbgsym Source: abyss Version: 2.3.10-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 32887 Depends: abyss (= 2.3.10-2) Section: debug Priority: optional Description: debug symbols for abyss Build-Ids: 01c4d955ea6ea8026e36d85f05942081074ee548 05e49436637480913d4e36c59f3ad8d75e51bcf8 093cab9c54b6ca131bfa6f7d8a637292561d4a89 099515158d94a91eca6c694637822153b1ba5bc3 0d1a66a71b1bd661b8ca91d37f6df25980e66f49 11dde0f56e4b6a0f18984424355dce54ac54121f 139db88e1f495c04c9d600e2a1f43a32d9b7f427 169903fd3a0b84d6cbd2bdd452b7c898f5ad31e8 1a29efe803a14ded3e30d6601bfa1d1beb06bff7 1d8d028151cd26b305eed56abad6bf0ce42aa841 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2026-03-28 20:29 ./usr/lib/debug/.dwz/x86_64-linux-gnu/abyss.debug drwxr-xr-x root/root 0 2026-03-28 20:29 ./usr/share/ drwxr-xr-x root/root 0 2026-03-28 20:29 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-03-28 20:29 ./usr/share/doc/abyss-dbgsym -> abyss abyss_2.3.10-2_amd64.deb ------------------------ new Debian package, version 2.0. size 3348676 bytes: control archive=2676 bytes. 711 bytes, 14 lines control 4847 bytes, 77 lines md5sums Package: abyss Version: 2.3.10-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 10067 Depends: make, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi40 (>= 5.0.10), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 14), perl:any, bsdextrautils, openmpi-common, openmpi-bin Section: science Priority: optional Homepage: https://github.com/bcgsc/abyss Description: de novo, parallel, sequence assembler for short reads ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread. drwxr-xr-x root/root 0 2026-03-28 20:29 ./ drwxr-xr-x root/root 0 2026-03-28 20:29 ./usr/ drwxr-xr-x root/root 0 2026-03-28 20:29 ./usr/bin/ -rwxr-xr-x root/root 145840 2026-03-28 20:29 ./usr/bin/DistanceEst -rwxr-xr-x root/root 133528 2026-03-28 20:29 ./usr/bin/abyss-fixmate -rwxr-xr-x root/root 23209 2026-03-28 20:29 ./usr/bin/abyss-pe drwxr-xr-x root/root 0 2026-03-28 20:29 ./usr/lib/ drwxr-xr-x root/root 0 2026-03-28 20:29 ./usr/lib/abyss/ -rwxr-xr-x root/root 264640 2026-03-28 20:29 ./usr/lib/abyss/ABYSS -rwxr-xr-x root/root 313792 2026-03-28 20:29 ./usr/lib/abyss/ABYSS-P -rwxr-xr-x root/root 178600 2026-03-28 20:29 ./usr/lib/abyss/AdjList -rwxr-xr-x root/root 80288 2026-03-28 20:29 ./usr/lib/abyss/Consensus -rwxr-xr-x root/root 104880 2026-03-28 20:29 ./usr/lib/abyss/DAssembler -rwxr-xr-x root/root 145840 2026-03-28 20:29 ./usr/lib/abyss/DistanceEst -rwxr-xr-x root/root 145840 2026-03-28 20:29 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root/root 1135 2026-03-28 20:29 ./usr/lib/abyss/abyss-bowtie -rwxr-xr-x root/root 1192 2026-03-28 20:29 ./usr/lib/abyss/abyss-bowtie2 -rwxr-xr-x root/root 1208 2026-03-28 20:29 ./usr/lib/abyss/abyss-bwa -rwxr-xr-x root/root 1454 2026-03-28 20:29 ./usr/lib/abyss/abyss-bwamem -rwxr-xr-x root/root 1362 2026-03-28 20:29 ./usr/lib/abyss/abyss-bwasw -rwxr-xr-x root/root 67984 2026-03-28 20:29 ./usr/lib/abyss/abyss-db-csv -rwxr-xr-x root/root 703 2026-03-28 20:29 ./usr/lib/abyss/abyss-db-txt -rwxr-xr-x root/root 2739 2026-03-28 20:29 ./usr/lib/abyss/abyss-dida -rwxr-xr-x root/root 84392 2026-03-28 20:29 ./usr/lib/abyss/abyss-fac -rwxr-xr-x root/root 2058 2026-03-28 20:29 ./usr/lib/abyss/abyss-fatoagp -rwxr-xr-x root/root 174512 2026-03-28 20:29 ./usr/lib/abyss/abyss-filtergraph -rwxr-xr-x root/root 133528 2026-03-28 20:29 ./usr/lib/abyss/abyss-fixmate -rwxr-xr-x root/root 133528 2026-03-28 20:29 ./usr/lib/abyss/abyss-fixmate-ssq -rwxr-xr-x root/root 104880 2026-03-28 20:29 ./usr/lib/abyss/abyss-gapfill -rwxr-xr-x root/root 88464 2026-03-28 20:29 ./usr/lib/abyss/abyss-gc -rwxr-xr-x root/root 92568 2026-03-28 20:29 ./usr/lib/abyss/abyss-index -rwxr-xr-x root/root 100760 2026-03-28 20:29 ./usr/lib/abyss/abyss-junction -rwxr-xr-x root/root 39 2026-03-28 20:29 ./usr/lib/abyss/abyss-kaligner -rwxr-xr-x root/root 133528 2026-03-28 20:29 ./usr/lib/abyss/abyss-layout -rwxr-xr-x root/root 104864 2026-03-28 20:29 ./usr/lib/abyss/abyss-longseqdist -rwxr-xr-x root/root 182696 2026-03-28 20:29 ./usr/lib/abyss/abyss-map -rwxr-xr-x root/root 186792 2026-03-28 20:29 ./usr/lib/abyss/abyss-map-ssq -rwxr-xr-x root/root 84408 2026-03-28 20:29 ./usr/lib/abyss/abyss-mergepairs -rwxr-xr-x root/root 207288 2026-03-28 20:29 ./usr/lib/abyss/abyss-overlap -rwxr-xr-x root/root 281032 2026-03-28 20:29 ./usr/lib/abyss/abyss-paired-dbg -rwxr-xr-x root/root 326080 2026-03-28 20:29 ./usr/lib/abyss/abyss-paired-dbg-mpi -rwxr-xr-x root/root 23209 2026-03-28 20:29 ./usr/lib/abyss/abyss-pe 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./usr/share/doc/abyss/test-data/ -rw-r--r-- root/root 743013 2026-03-28 20:29 ./usr/share/doc/abyss/test-data/reads1.fastq.gz -rw-r--r-- root/root 743377 2026-03-28 20:29 ./usr/share/doc/abyss/test-data/reads2.fastq.gz drwxr-xr-x root/root 0 2026-03-28 20:29 ./usr/share/man/ drwxr-xr-x root/root 0 2026-03-28 20:29 ./usr/share/man/man1/ -rw-r--r-- root/root 1021 2026-03-28 20:29 ./usr/share/man/man1/DistanceEst.1.gz -rw-r--r-- root/root 790 2026-03-28 20:29 ./usr/share/man/man1/abyss-fixmate.1.gz -rw-r--r-- root/root 3562 2026-03-28 20:29 ./usr/share/man/man1/abyss-pe.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 29 Mar 2026 04:09:37 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 29 Mar 2026 04:09:37 +0000 | +------------------------------------------------------------------------------+ Purging /build/abyss-BQNOuM Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 29 Mar 2026 04:09:38 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 768264 Build-Time: 429 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 19 Job: /srv/debomatic/incoming/abyss_2.3.10-2.dsc Machine Architecture: amd64 Package: abyss Package-Time: 452 Source-Version: 2.3.10-2 Space: 768264 Status: successful Version: 2.3.10-2 -------------------------------------------------------------------------------- Finished at 2026-03-29T04:09:36Z Build needed 00:07:32, 768264k disk space