sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | abyss 2.3.10-1 (amd64) Sun, 17 Aug 2025 06:23:54 +0000 | +==============================================================================+ Package: abyss Version: 2.3.10-1 Source Version: 2.3.10-1 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, 17 Aug 2025 06:23:55 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup abyss_2.3.10-1 perl-5.42-throwaway amd64 --------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup abyss_2.3.10-1 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 17 Aug 2025 06:23:55 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:2 http://deb.debian.org/debian unstable InRelease [216 kB] Get:3 http://deb.debian.org/debian sid InRelease [216 kB] Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:5 file:/srv/reprepro perl-5.42/main amd64 Packages [541 kB] Get:6 http://deb.debian.org/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-17-0209.32-F-2025-08-16-2015.43.pdiff [65.4 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-17-0209.32-F-2025-08-16-2015.43.pdiff [50.3 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-17-0209.32-F-2025-08-16-2015.43.pdiff [65.4 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-17-0209.32-F-2025-08-16-2015.43.pdiff [50.3 kB] Fetched 674 kB in 3s (250 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu init-system-helpers libbinutils libctf-nobfd0 libctf0 libgprofng0 libidn2-0 libldap2 libsframe2 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5687 kB/5881 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 libldap2 amd64 2.6.10+dfsg-1+b1 [194 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.45-4 [810 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.45-4 [89.7 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.45-4 [157 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.45-4 [1042 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.45-4 [266 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.45-4 [539 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.45-4 [2556 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libsframe2 amd64 2.45-4 [79.5 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-3 [109 kB] Fetched 5687 kB in 0s (123 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14971 files and directories currently installed.) Preparing to unpack .../0-libgprofng0_2.45-4_amd64.deb ... Unpacking libgprofng0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../1-libctf0_2.45-4_amd64.deb ... Unpacking libctf0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../2-libctf-nobfd0_2.45-4_amd64.deb ... Unpacking libctf-nobfd0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../3-binutils-x86-64-linux-gnu_2.45-4_amd64.deb ... Unpacking binutils-x86-64-linux-gnu (2.45-4) over (2.45-3) ... Preparing to unpack .../4-binutils_2.45-4_amd64.deb ... Unpacking binutils (2.45-4) over (2.45-3) ... Preparing to unpack .../5-libbinutils_2.45-4_amd64.deb ... Unpacking libbinutils:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../6-binutils-common_2.45-4_amd64.deb ... Unpacking binutils-common:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../7-libsframe2_2.45-4_amd64.deb ... Unpacking libsframe2:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../8-libidn2-0_2.3.8-3_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-3) over (2.3.8-2) ... Preparing to unpack .../9-libldap2_2.6.10+dfsg-1+b1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1+b1) over (2.6.10+dfsg-1) ... Setting up libsframe2:amd64 (2.45-4) ... Setting up binutils-common:amd64 (2.45-4) ... Setting up libctf-nobfd0:amd64 (2.45-4) ... Setting up libidn2-0:amd64 (2.3.8-3) ... Setting up libbinutils:amd64 (2.45-4) ... Setting up libldap2:amd64 (2.6.10+dfsg-1+b1) ... Setting up libctf0:amd64 (2.45-4) ... Setting up libgprofng0:amd64 (2.45-4) ... Setting up binutils-x86-64-linux-gnu (2.45-4) ... Setting up binutils (2.45-4) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Fetch source files Sun, 17 Aug 2025 06:24:01 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/abyss_2.3.10-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 17 Aug 2025 06:24:01 +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-TAe4SE/resolver-7wXtQf/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/abyss-TAe4SE/resolver-7wXtQf/apt_archive ./ InRelease Get:2 copy:/build/abyss-TAe4SE/resolver-7wXtQf/apt_archive ./ Release [609 B] Ign:3 copy:/build/abyss-TAe4SE/resolver-7wXtQf/apt_archive ./ Release.gpg Get:4 copy:/build/abyss-TAe4SE/resolver-7wXtQf/apt_archive ./ Sources [777 B] Get:5 copy:/build/abyss-TAe4SE/resolver-7wXtQf/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... 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-14 gfortran-14-x86-64-linux-gnu groff-base help2man ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libboost-graph-dev libboost-graph1.83-dev libboost-graph1.83.0 libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-test1.83-dev libboost-test1.83.0 libboost1.83-dev libbrotli1 libbtllib-dev libcbor0.10 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-14-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhtml-parser-perl libhtml-tagset-perl libhts3t64 libhtscodecs2 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu76 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 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 libpkgconf3 libpmix-dev libpmix2t64 libpsl5t64 libpsm2-2 librdmacm1t64 librtmp1 libsparsehash-dev libsqlite3-dev libssh2-1t64 libtext-markdown-perl libtext-multimarkdown-perl libtool libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-16 libxnvctrl0 libz3-4 libze1 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkgconf pkgconf-bin po-debconf samtools sensible-utils wget zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n gfortran-14-multilib gfortran-14-doc libcoarrays-dev groff graphviz libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-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 gcj-jdk libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libwww-perl m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl cwltool Recommended packages: libsdsl-dev ca-certificates libarchive-cpio-perl libhttp-message-perl javascript-common krb5-locales libgpm2 libcoarrays-openmpi-dev publicsuffix xauth libmail-sendmail-perl 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-14 gfortran-14-x86-64-linux-gnu groff-base help2man ibverbs-providers icu-devtools intltool-debian libamd-comgr2 libamdhip64-5 libarchive-zip-perl libboost-graph-dev libboost-graph1.83-dev libboost-graph1.83.0 libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-test1.83-dev libboost-test1.83.0 libboost1.83-dev libbrotli1 libbtllib-dev libcbor0.10 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-14-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhsakmt1 libhtml-parser-perl libhtml-tagset-perl libhts3t64 libhtscodecs2 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libicu-dev libicu76 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm17t64 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 libpkgconf3 libpmix-dev libpmix2t64 libpsl5t64 libpsm2-2 librdmacm1t64 librtmp1 libsparsehash-dev libsqlite3-dev libssh2-1t64 libtext-markdown-perl libtext-multimarkdown-perl libtool libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-16 libxnvctrl0 libz3-4 libze1 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkgconf pkgconf-bin po-debconf samtools sbuild-build-depends-main-dummy sensible-utils wget zlib1g-dev 0 upgraded, 143 newly installed, 0 to remove and 0 not upgraded. Need to get 140 MB/140 MB of archives. After this operation, 705 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 liblocale-gettext-perl amd64 1.07-7+b2 [15.3 kB] Get:2 copy:/build/abyss-TAe4SE/resolver-7wXtQf/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B] Get:3 file:/srv/reprepro perl-5.42/main amd64 libhtml-parser-perl amd64 3.83-1+b3 [100 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-1 [94.7 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20250104-1 [93.8 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.16.0-2 [78.8 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:21 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.0p1-8 [986 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 wget amd64 1.25.0-2 [984 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get:27 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.25 [91.6 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:38 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.1 [640 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.25 [937 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-1 [862 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.3.0-5 [879 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.3.0-5 [11.7 MB] Get:48 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.3.0-5 [15.2 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-2 [59.4 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-2 [182 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 56.1-1 [62.4 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 56.1-1 [357 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-4 [9722 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 76.1-4 [215 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-22+b2 [23.6 MB] Get:59 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get:60 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.124-2 [8288 B] Get:61 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.124-2 [39.0 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.124-2 [22.6 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1 [22.2 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.2.4+ds-1 [61.1 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-3 [535 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-6 [8924 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Get:68 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83.0 amd64 1.83.0-4.2 [359 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-4.2 [330 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 76.1-4 [10.8 MB] Get:71 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-4.2 [346 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4.2 [333 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4.2 [373 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-4.2 [471 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-4.2 [541 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83-dev amd64 1.83.0-4.2 [383 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B] Get:78 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libcpptoml-dev all 0.1.1-3 [180 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.21-1 [667 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libbtllib-dev amd64 1.7.5+dfsg-2 [218 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 56.1-1 [70.4 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1 [706 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libfuse3-4 amd64 3.17.3-1 [99.0 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.30-1 [105 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.12.0-4+b1 [164 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.19-1 [36.5 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-4 [416 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.5.4-4 [168 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.12.0-4+b1 [257 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.12.0-4+b1 [23.7 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 56.1-1 [30.0 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 56.1-1 [44.5 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-2 [101 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-2 [201 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 56.1-1 [654 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.16-1 [19.7 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 6.0.0-2 [676 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.18.1+ds-2+b1 [1196 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.7-1 [2365 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.7-1 [97.2 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 6.0.0-2 [4380 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.7-1 [189 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.7-1 [1089 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-7 [1109 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 libtext-markdown-perl all 1.000031-5 [31.4 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 libtext-multimarkdown-perl all 1.000035-3 [28.5 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Preconfiguring packages ... Fetched 140 MB in 1s (169 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 14972 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-7+b2_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../003-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. 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Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libnl-3-200:amd64 (3.7.0-2) ... Setting up libboost-graph1.83.0:amd64 (1.83.0-4.2) ... Setting up libpsm2-2 (11.2.185-2.1) ... Setting up openmpi-common (5.0.7-1) ... Setting up libx11-6:amd64 (2:1.8.12-1) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libicu76:amd64 (76.1-4) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfuse3-4:amd64 (3.17.3-1) ... Setting up libfido2-1:amd64 (1.16.0-2) ... Setting up libdrm-common (2.4.124-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up liburi-perl (5.30-1) ... Setting up liblocale-gettext-perl (1.07-7+b2) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:amd64 (14.3.0-5) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up wget (1.25.0-2) ... Setting up libtool (2.5.4-4) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-4.2) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libboost-test1.83-dev:amd64 (1.83.0-4.2) ... Setting up gfortran-14-x86-64-linux-gnu (14.3.0-5) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.19-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-2) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b2) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.5.4-4) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libllvm17t64:amd64 (1:17.0.6-22+b2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up icu-devtools (76.1-4) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libdrm2:amd64 (2.4.124-2) ... Setting up libnl-3-dev:amd64 (3.7.0-2) ... Setting up groff-base (1.23.0-9) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b3) ... Setting up libhwloc-dev:amd64 (2.12.0-4+b1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up gfortran-14 (14.3.0-5) ... Setting up libtext-multimarkdown-perl (1.000035-3) ... Setting up libicu-dev:amd64 (76.1-4) ... Setting up libdrm-amdgpu1:amd64 (2.4.124-2) ... Setting up libibverbs1:amd64 (56.1-1) ... Setting up ibverbs-providers:amd64 (56.1-1) ... Setting up openssh-client (1:10.0p1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.15.0-1) ... Setting up libhwloc-plugins:amd64 (2.12.0-4+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnl-route-3-dev:amd64 (3.7.0-2) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-4.2) ... Setting up libpmix2t64:amd64 (6.0.0-2) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up librdmacm1t64:amd64 (56.1-1) ... Setting up libpmix-dev:amd64 (6.0.0-2) ... Setting up libhsakmt1:amd64 (6.2.4+ds-1) ... Setting up libfabric1:amd64 (2.1.0-1.1) ... Setting up debhelper (13.25) ... Setting up libibverbs-dev:amd64 (56.1-1) ... Setting up libboost-graph1.83-dev:amd64 (1.83.0-4.2) ... Setting up samtools (1.21-1) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ... Setting up libboost-graph-dev:amd64 (1.83.0.2+b2) ... Setting up libbtllib-dev (1.7.5+dfsg-2) ... Setting up libamdhip64-5:amd64 (5.7.1-6) ... Setting up libucx0:amd64 (1.18.1+ds-2+b1) ... Setting up libopenmpi40:amd64 (5.0.7-1) ... Setting up openmpi-bin (5.0.7-1) ... 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) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (5.0.7-1) ... 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 (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 17 Aug 2025 06:24:17 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sun, 17 Aug 2025 06:24:17 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.45-4 dpkg-dev_1.22.21 g++-14_14.3.0-5 gcc-14_14.3.0-5 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 linux-libc-dev_6.12.38-1 Package versions: adduser_3.152 apt_3.1.4 architecture-properties_0.2.6 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.7 bash_5.2.37-2+b5 binutils_2.45-4 binutils-common_2.45-4 binutils-gold_2.44-2 binutils-gold-x86-64-linux-gnu_2.44-2 binutils-x86-64-linux-gnu_2.45-4 bsdextrautils_2.41.1-1 bsdutils_1:2.41.1-1 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-14_14.3.0-5 cpp-14-x86-64-linux-gnu_14.3.0-5 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.25 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.8-2 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.3.0-5 g++-14-x86-64-linux-gnu_14.3.0-5 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.3.0-5 gcc-14-base_14.3.0-5 gcc-14-x86-64-linux-gnu_14.3.0-5 gcc-15-base_15.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 gfortran-14_14.3.0-5 gfortran-14-x86-64-linux-gnu_14.3.0-5 gnupg_2.4.8-2 gnupg-l10n_2.4.8-2 gpg_2.4.8-2 gpg-agent_2.4.8-2 gpgconf_2.4.8-2 gpgsm_2.4.8-2 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 help2man_1.49.3 hostname_3.25 ibverbs-providers_56.1-1 icu-devtools_76.1-4 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libamd-comgr2_6.0+git20231212.4510c28+dfsg-3+b2 libamdhip64-5_5.7.1-6 libapt-pkg7.0_3.1.4 libarchive-zip-perl_1.68-1 libasan8_15.2.0-1 libassuan9_3.0.2-2 libatomic1_15.2.0-1 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.45-4 libblkid1_2.41.1-1 libboost-graph-dev_1.83.0.2+b2 libboost-graph1.83-dev_1.83.0-4.2 libboost-graph1.83.0_1.83.0-4.2 libboost-regex1.83-dev_1.83.0-4.2 libboost-regex1.83.0_1.83.0-4.2 libboost-serialization1.83-dev_1.83.0-4.2 libboost-serialization1.83.0_1.83.0-4.2 libboost-test1.83-dev_1.83.0-4.2 libboost-test1.83.0_1.83.0-4.2 libboost1.83-dev_1.83.0-4.2 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbtllib-dev_1.7.5+dfsg-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcbor0.10_0.10.2-2 libcc1-0_15.2.0-1 libcom-err2_1.47.2-3+b3 libcpptoml-dev_0.1.1-3 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-4 libctf0_2.45-4 libcurl3t64-gnutls_8.15.0-1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.280 libdebhelper-perl_13.25 libdeflate0_1.23-2 libdpkg-perl_1.22.21 libdrm-amdgpu1_2.4.124-2 libdrm-common_2.4.124-2 libdrm2_2.4.124-2 libeatmydata1_131-2+b1 libedit2_3.1-20250104-1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libevent-core-2.1-7t64_2.1.12-stable-10+b1 libevent-dev_2.1.12-stable-10+b1 libevent-extra-2.1-7t64_2.1.12-stable-10+b1 libevent-openssl-2.1-7t64_2.1.12-stable-10+b1 libevent-pthreads-2.1-7t64_2.1.12-stable-10+b1 libfabric1_2.1.0-1.1 libffi8_3.4.8-2 libfido2-1_1.16.0-2 libfile-stripnondeterminism-perl_1.14.1-2 libfuse3-4_3.17.3-1 libgcc-14-dev_14.3.0-5 libgcc-s1_15.2.0-1 libgcrypt20_1.11.2-2 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran-14-dev_14.3.0-5 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libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe2_2.45-4 libsmartcols1_2.41.1-1 libsparsehash-dev_2.0.3-2 libsqlite3-0_3.46.1-7 libsqlite3-dev_3.46.1-7 libssh2-1t64_1.11.1-1 libssl3t64_3.5.2-1 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 libsystemd0_258~rc2-2 libtasn1-6_4.20.0-2 libtext-markdown-perl_1.000031-5 libtext-multimarkdown-perl_1.000035-3 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_15.2.0-1 libubsan1_15.2.0-1 libuchardet0_0.0.8-1+b2 libucx0_1.18.1+ds-2+b1 libudev1_258~rc2-2 libunistring5_1.3-2 liburi-perl_5.30-1 libuuid1_2.41.1-1 libx11-6_2:1.8.12-1 libx11-data_2:1.8.12-1 libxau6_1:1.0.11-1 libxcb1_1.17.0-2+b1 libxdmcp6_1:1.1.5-1 libxext6_2:1.3.4-1+b3 libxml2_2.12.7+dfsg+really2.9.14-2.1 libxml2-16_2.14.5+dfsg-0.1 libxnvctrl0_535.171.04-1+b2 libxxhash0_0.8.3-2 libz3-4_4.13.3-1 libze1_1.24.1-2 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.38-1 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 ocl-icd-libopencl1_2.3.3-1 openmpi-bin_5.0.7-1 openmpi-common_5.0.7-1 openssh-client_1:10.0p1-8 openssl-provider-legacy_3.5.2-1 passwd_1:4.17.4-2 patch_2.8-2 perl_5.42.0-1 perl-base_5.42.0-1 perl-modules-5.40_5.40.1-6 perl-modules-5.42_5.42.0-1 pinentry-curses_1.3.2-3 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 samtools_1.21-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 util-linux_2.41.1-1 wget_1.25.0-2 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Sun, 17 Aug 2025 06:24:17 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: abyss Binary: abyss Architecture: any Version: 2.3.10-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://github.com/bcgsc/abyss Standards-Version: 4.7.0 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 ee4818b5a88ed0615520b35f0e31b46c11b2f425 1497940 abyss_2.3.10-1.debian.tar.xz Checksums-Sha256: c8461eb017edfbd83c2aac9910da438df2d79660d2e87ab289f2de7a0d620a4c 933928 abyss_2.3.10.orig.tar.xz e809ab4f042a43c439cf94d2650264bc7d055042e8168c093a75293aa4f33c4a 1497940 abyss_2.3.10-1.debian.tar.xz Files: b13b49e294474086d2e1395f5689843b 933928 abyss_2.3.10.orig.tar.xz 7534eff746ccb91f0acac3cb29c24422 1497940 abyss_2.3.10-1.debian.tar.xz Dgit: 17da39574845c0e2f27363979a61f3402545ddb8 debian archive/debian/2.3.10-1 https://git.dgit.debian.org/abyss -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmcmKLsUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoNhhAAh7JJZI6fYcVIfVxhh3a6X5otjS0L YJ5ULejgvjt5NQLF8V3+ximRf7sPM2a75tQekfrRikg1Z3AjgFxBnTsi2cUL5u4O NcjXa/qsGWjyPOnxo36Agr0wLfCnjQCp+W05gl+LLq+V/IXAHP8pS5WKVOFpNkbF u4+0Dwr8Rr4zVpJLjt1uaBL7bUJloBK9+HwIfjvicBl9YNn+klPLLToqACwY+iXe R5NhHnQra7XpbzSCoVqvTtjJxxZrAZ5P5kb8bf96mKJWObYfFA+FKzlsa2lKy2vF We936R+VSpxEzxtI5m5k5SuH3kEQ9siTh2imXY0oEupKrfxoODXtriA8fv1n5Rl8 IdyxP86ot9pApvJYem57MSoObHB28E6QRUmfoQVDcp6eXKq6QSrq+eaEYSrK//IL MCrpeVrjXcKsFYr+m7TP2mGqV3xNZCQSmwD/ByUIq+z+K8mIL/ueOPeubVjnOdgK 0sFPPpxL/Gge+M67JavzuTWBxuSxe7Gxx311OYuoVZ6ZXbjuuUyBzNYoci8/odnU 73auPStQ81HhPDhKkOjpYd2d43ciKYQKH1evEzbAzN9/AOZZMI6S1nSzk93dhOd9 6KhrtjDoy//eHedOu8fbnDU5r18vsQzOHE7qVdcjKVgLXp4zQDN50oyxnu/IjleR qUkm0T2hTjCJGyc= =6QEG -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./abyss_2.3.10-1.dsc: no acceptable signature found dpkg-source: info: extracting abyss in /build/abyss-TAe4SE/abyss-2.3.10 dpkg-source: info: unpacking abyss_2.3.10.orig.tar.xz dpkg-source: info: unpacking abyss_2.3.10-1.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 Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Sun, 17 Aug 2025 06:24:18 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network abyss_2.3.10-1 perl-5.42-throwaway amd64 --------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network abyss_2.3.10-1 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent 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-TAe4SE/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-38302566-c854-4635-9557-7e0857b36dae 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 2.3.10-1 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_2.3.10-1.debian.tar.xz dpkg-source: info: building abyss in abyss_2.3.10-1.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf 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' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10' debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10' dh_auto_build make -j2 make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10' make all-recursive make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10' Making all in bin make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/bin' Making all in doc make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/doc' Making all in Common make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/Common' Making all in Graph make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Graph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/Graph' Making all in DataLayer make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/FMIndex' Making all in Assembly make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/Assembly' Making all in dialign make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/dialign' Making all in Align make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Align' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/Align' Making all in ABYSS make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/ABYSS' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/ABYSS' Making all in Parallel make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Parallel' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/Parallel' Making all in Bloom make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Bloom' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/BloomDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Konnector' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/Konnector' Making all in Consensus make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Consensus' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/Consensus' Making all in DAssembler make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DAssembler' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DistanceEst' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/KAligner' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/KAligner' Making all in Layout make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Layout' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/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-TAe4SE/abyss-2.3.10/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/LogKmerCount' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/LogKmerCount' Making all in Map make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Map' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/Map' Making all in MergePaths make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/MergePaths' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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 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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/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 g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/MergePaths' Making all in Overlap make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Overlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, scaffoldGraph, DirectedGraph::out_edge_iterator(e))’ 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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/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-TAe4SE/abyss-2.3.10/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PairedDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/ParseAligns' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PathOverlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/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-TAe4SE/abyss-2.3.10/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PopBubbles' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/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-TAe4SE/abyss-2.3.10/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Scaffold' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/SimpleGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/kmerprint' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/FilterGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/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-TAe4SE/abyss-2.3.10/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/GapFiller' Making all in Sealer make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Sealer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/Sealer' Making all in RResolver make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/RResolver' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/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-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/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-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/RResolver' Making all in AdjList make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/AdjList' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/abyss-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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: the temporary was destroyed at the end of the full expression ‘get >(boost::edge_bundle, (* & g), DirectedGraph::out_edge_iterator(e))’ 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-TAe4SE/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-TAe4SE/abyss-2.3.10/AdjList' Making all in vendor make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Unittest' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10' make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10' markdown README.md > README.html make[1]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10' dh_auto_test make -j2 check "TESTSUITEFLAGS=-j2 --verbose" VERBOSE=1 make[1]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10' Making check in bin make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/bin' Making check in doc make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/doc' Making check in Common make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Common' Making check in Graph make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Graph' Making check in DataLayer make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DataLayer' Making check in DataBase make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DataBase' Making check in FMIndex make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/FMIndex' Making check in Assembly make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Assembly' Making check in dialign make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/dialign' Making check in Align make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Align' Making check in ABYSS make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/ABYSS' Making check in Parallel make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Parallel' Making check in Bloom make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Bloom' Making check in BloomDBG make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/BloomDBG' Making check in Konnector make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Konnector' Making check in Consensus make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Consensus' Making check in DAssembler make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/KAligner' Making check in Layout make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/LogKmerCount' Making check in Map make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Map' Making check in MergePaths make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/MergePaths' Making check in Overlap make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Overlap' Making check in PairedDBG make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/GapFiller' Making check in Sealer make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Sealer' Making check in RResolver make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/RResolver' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/RResolver' Making check in AdjList make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/AdjList' Making check in vendor make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor' Making check in vendor/gtest-1.7.0 make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/vendor/gtest-1.7.0' make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-TAe4SE/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/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-TAe4SE/abyss-2.3.10/Unittest' make check-TESTS make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Unittest' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Unittest' PASS: common_stringutil PASS: common_histogram PASS: common_bitutil PASS: common_kmer PASS: common_KmerIterator PASS: common_sequence PASS: common_sam PASS: common_sam_ssq PASS: BloomFilter PASS: Konnector_DBGBloomAlgorithms PASS: Konnector_DBGBloom PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_ExtendPath PASS: graph_DotIO PASS: graph_UndirectedGraph PASS: Konnector_konnector PASS: PairedDBG_LoadAlgorithm PASS: DBG_LoadAlgorithm PASS: PairedDBG_Dinuc PASS: PairedDBG_KmerPair PASS: BloomDBG_BloomDBG PASS: PairedDBG_BranchRecord 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-TAe4SE/abyss-2.3.10/Unittest' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Unittest' make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Unittest' make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10' make[2]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10' make[1]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10' dh_auto_install --destdir=debian/tmp make -j2 install DESTDIR=/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10' Making install in bin make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/bin' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/bin' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/bin' Making install in doc make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/doc' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/doc' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/doc' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/doc' Making install in Common make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Common' make[4]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/Common' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Common' Making install in Graph make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Graph' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Graph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Graph' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Graph' Making install in DataLayer make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DataLayer' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DataLayer' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DataLayer' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DataLayer' Making install in DataBase make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DataBase' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DataBase' /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-db-csv '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DataBase' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DataBase' Making install in FMIndex make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/FMIndex' make[4]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/FMIndex' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/FMIndex' Making install in Assembly make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Assembly' make[4]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/Assembly' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Assembly' Making install in dialign make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/dialign' make[4]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/dialign' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/dialign' Making install in Align make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Align' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Align' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Align' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Align' Making install in ABYSS make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/ABYSS' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/ABYSS' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/ABYSS' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Parallel' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Parallel' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Parallel' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Parallel' Making install in Bloom make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Bloom' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Bloom' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Bloom' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/BloomDBG' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/BloomDBG' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Konnector' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Konnector' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Konnector' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Consensus' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Consensus' /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Consensus '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Consensus' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DAssembler' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DAssembler' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DistanceEst' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DistanceEst' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/KAligner' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/KAligner' /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c KAligner '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/KAligner' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/KAligner' Making install in Layout make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Layout' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Layout' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Layout' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/LogKmerCount' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/LogKmerCount' /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c logcounter '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/LogKmerCount' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Map' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Map' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Map' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Map' Making install in MergePaths make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/MergePaths' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/MergePaths' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/MergePaths' Making install in Overlap make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Overlap' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Overlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Overlap' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PairedDBG' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/PairedDBG' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/ParseAligns' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/ParseAligns' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PathOverlap' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/PathOverlap' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PopBubbles' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/PopBubbles' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Scaffold' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Scaffold' /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Scaffold' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/SimpleGraph' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/SimpleGraph' /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c SimpleGraph '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/SimpleGraph' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/kmerprint' make[4]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/kmerprint' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/FilterGraph' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/FilterGraph' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/GapFiller' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/GapFiller' /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-gapfill '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/GapFiller' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/GapFiller' Making install in Sealer make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Sealer' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Sealer' /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Sealer' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Sealer' Making install in RResolver make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/RResolver' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/RResolver' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-rresolver-short '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/RResolver' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/RResolver' Making install in AdjList make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/AdjList' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/AdjList' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/abyss-TAe4SE/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/AdjList' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/AdjList' Making install in vendor make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor' make[4]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/vendor' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor/gtest-1.7.0' make[4]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/vendor/gtest-1.7.0' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/vendor/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10/Unittest' make[4]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/Unittest' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10/Unittest' make[3]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10' make[4]: Entering directory '/build/abyss-TAe4SE/abyss-2.3.10' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10' make[3]: Leaving directory '/build/abyss-TAe4SE/abyss-2.3.10' make[2]: Leaving directory '/build/abyss-TAe4SE/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-TAe4SE/abyss-2.3.10' debian/rules override_dh_install make[1]: Entering directory '/build/abyss-TAe4SE/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-TAe4SE/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_2.3.10-1_amd64.deb'. dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.10-1_amd64.deb'. dpkg-genbuildinfo -O../abyss_2.3.10-1_amd64.buildinfo dpkg-genchanges -O../abyss_2.3.10-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2025-08-17T06:29:58Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 17 Aug 2025 06:29:59 +0000 | +------------------------------------------------------------------------------+ abyss_2.3.10-1_amd64.changes: ----------------------------- Format: 1.8 Date: Sat, 02 Nov 2024 14:00:42 +0100 Source: abyss Binary: abyss abyss-dbgsym Architecture: source amd64 Version: 2.3.10-1 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 Changes: abyss (2.3.10-1) unstable; urgency=medium . * New upstream version 2.3.10 * fix-privacy-breach.patch: refresh. * d/manpages: install abyss-pe.1. * abyss-pe.patch: declare forwarding not needed. Checksums-Sha1: 00ab9da6f009d23c74c90856baa06c3ca0f23e52 1286 abyss_2.3.10-1.dsc 2179eef8d6120588e46efb7397cc7ba3cfca5c26 933928 abyss_2.3.10.orig.tar.xz 9eb56e567c4210de1596221d13a498003ebbae61 1497948 abyss_2.3.10-1.debian.tar.xz fe2da30001cb907cd23dc8dcaa1ee83d296e1df6 30455224 abyss-dbgsym_2.3.10-1_amd64.deb a63f20057667bd8d4e812ef2bb9f17ed77af82df 9154 abyss_2.3.10-1_amd64.buildinfo ea7de8e274ee233fa2670f0cc29c63ad22de4376 3340300 abyss_2.3.10-1_amd64.deb Checksums-Sha256: deba229064b68c361c5c34015a0d38c3908d8826c1655fc937df405ee6bf6f38 1286 abyss_2.3.10-1.dsc c8461eb017edfbd83c2aac9910da438df2d79660d2e87ab289f2de7a0d620a4c 933928 abyss_2.3.10.orig.tar.xz b2e21bf64a69fcbfac0fbe12573288bedeb34e1b482b4678221b8fad9777c173 1497948 abyss_2.3.10-1.debian.tar.xz d8725441ae63dcb952189c6b6affbf8dd579cf5661910d530fec37b6b683164d 30455224 abyss-dbgsym_2.3.10-1_amd64.deb e854066e1f5447ed8593b259e53eccb6a1a2fa5114af5c54200170ce78b835fb 9154 abyss_2.3.10-1_amd64.buildinfo a4a05162edaacb21da398651e60e83e006871caca3d07364b4e9b63716dd5b13 3340300 abyss_2.3.10-1_amd64.deb Files: 4041b5dda93dc02925bb0c1fcc3d8a03 1286 science optional abyss_2.3.10-1.dsc b13b49e294474086d2e1395f5689843b 933928 science optional abyss_2.3.10.orig.tar.xz 3bd08be3315fd7d5716832479e91f1d3 1497948 science optional abyss_2.3.10-1.debian.tar.xz 4db37af9e3a5908f367013d5bc093109 30455224 debug optional abyss-dbgsym_2.3.10-1_amd64.deb 4cab3c554901c6ef6f0d6f7a30c443de 9154 science optional abyss_2.3.10-1_amd64.buildinfo aa2c025b21c5e4266bec00b461f56e5c 3340300 science optional abyss_2.3.10-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 17 Aug 2025 06:29:59 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: abyss Binary: abyss abyss-dbgsym Architecture: amd64 source Version: 2.3.10-1 Checksums-Md5: 4041b5dda93dc02925bb0c1fcc3d8a03 1286 abyss_2.3.10-1.dsc 4db37af9e3a5908f367013d5bc093109 30455224 abyss-dbgsym_2.3.10-1_amd64.deb aa2c025b21c5e4266bec00b461f56e5c 3340300 abyss_2.3.10-1_amd64.deb Checksums-Sha1: 00ab9da6f009d23c74c90856baa06c3ca0f23e52 1286 abyss_2.3.10-1.dsc fe2da30001cb907cd23dc8dcaa1ee83d296e1df6 30455224 abyss-dbgsym_2.3.10-1_amd64.deb ea7de8e274ee233fa2670f0cc29c63ad22de4376 3340300 abyss_2.3.10-1_amd64.deb Checksums-Sha256: deba229064b68c361c5c34015a0d38c3908d8826c1655fc937df405ee6bf6f38 1286 abyss_2.3.10-1.dsc d8725441ae63dcb952189c6b6affbf8dd579cf5661910d530fec37b6b683164d 30455224 abyss-dbgsym_2.3.10-1_amd64.deb a4a05162edaacb21da398651e60e83e006871caca3d07364b4e9b63716dd5b13 3340300 abyss_2.3.10-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 17 Aug 2025 06:29:58 +0000 Build-Path: /build/abyss-TAe4SE/abyss-2.3.10 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.152), architecture-properties (= 0.2.6), autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.7), bash (= 5.2.37-2+b5), binutils (= 2.45-4), binutils-common (= 2.45-4), binutils-x86-64-linux-gnu (= 2.45-4), bsdextrautils (= 2.41.1-1), bsdutils (= 1:2.41.1-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-14 (= 14.3.0-5), cpp-14-x86-64-linux-gnu (= 14.3.0-5), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.25), debianutils (= 5.23.2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.3.0-5), g++-14-x86-64-linux-gnu (= 14.3.0-5), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.3.0-5), gcc-14-base (= 14.3.0-5), gcc-14-x86-64-linux-gnu (= 14.3.0-5), gcc-15-base (= 15.2.0-1), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), gfortran-14 (= 14.3.0-5), gfortran-14-x86-64-linux-gnu (= 14.3.0-5), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), ibverbs-providers (= 56.1-1), icu-devtools (= 76.1-4), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libamd-comgr2 (= 6.0+git20231212.4510c28+dfsg-3+b2), libamdhip64-5 (= 5.7.1-6), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-1), libatomic1 (= 15.2.0-1), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbinutils (= 2.45-4), libblkid1 (= 2.41.1-1), libboost-graph-dev (= 1.83.0.2+b2), libboost-graph1.83-dev (= 1.83.0-4.2), libboost-graph1.83.0 (= 1.83.0-4.2), libboost-regex1.83-dev (= 1.83.0-4.2), libboost-regex1.83.0 (= 1.83.0-4.2), libboost-serialization1.83-dev (= 1.83.0-4.2), libboost-serialization1.83.0 (= 1.83.0-4.2), libboost-test1.83-dev (= 1.83.0-4.2), libboost-test1.83.0 (= 1.83.0-4.2), libboost1.83-dev (= 1.83.0-4.2), libbrotli1 (= 1.1.0-2+b7), libbsd0 (= 0.12.2-2), libbtllib-dev (= 1.7.5+dfsg-2), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcbor0.10 (= 0.10.2-2), libcc1-0 (= 15.2.0-1), libcom-err2 (= 1.47.2-3+b3), libcpptoml-dev (= 0.1.1-3), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.45-4), libctf0 (= 2.45-4), libcurl3t64-gnutls (= 8.15.0-1), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.25), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.21), libdrm-amdgpu1 (= 2.4.124-2), libdrm-common (= 2.4.124-2), libdrm2 (= 2.4.124-2), libedit2 (= 3.1-20250104-1), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-core-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-dev (= 2.1.12-stable-10+b1), libevent-extra-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-openssl-2.1-7t64 (= 2.1.12-stable-10+b1), libevent-pthreads-2.1-7t64 (= 2.1.12-stable-10+b1), libfabric1 (= 2.1.0-1.1), libffi8 (= 3.4.8-2), libfido2-1 (= 1.16.0-2), libfile-stripnondeterminism-perl (= 1.14.1-2), libfuse3-4 (= 3.17.3-1), libgcc-14-dev (= 14.3.0-5), libgcc-s1 (= 15.2.0-1), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgfortran-14-dev (= 14.3.0-5), libgfortran5 (= 15.2.0-1), libgmp10 (= 2:6.3.0+dfsg-3), libgnutls30t64 (= 3.8.10-2), libgomp1 (= 15.2.0-1), libgprofng0 (= 2.45-4), libgssapi-krb5-2 (= 1.21.3-5), libhogweed6t64 (= 3.10.1-1), libhsa-runtime64-1 (= 6.1.2-3), libhsakmt1 (= 6.2.4+ds-1), libhtml-parser-perl (= 3.83-1+b3), libhtml-tagset-perl (= 3.24-1), libhts3t64 (= 1.21+ds-1), libhtscodecs2 (= 1.6.1-2), libhwasan0 (= 15.2.0-1), libhwloc-dev (= 2.12.0-4+b1), libhwloc-plugins (= 2.12.0-4+b1), libhwloc15 (= 2.12.0-4+b1), libibmad5 (= 56.1-1), libibumad3 (= 56.1-1), libibverbs-dev (= 56.1-1), libibverbs1 (= 56.1-1), libicu-dev (= 76.1-4), libicu76 (= 76.1-4), libidn2-0 (= 2.3.8-3), libisl23 (= 0.27-1), libitm1 (= 15.2.0-1), libjansson4 (= 2.14-2+b3), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-jquery-ui (= 1.13.2+dfsg-1), libk5crypto3 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), liblastlog2-2 (= 2.41.1-1), libldap2 (= 2.6.10+dfsg-1+b1), libllvm17t64 (= 1:17.0.6-22+b2), liblocale-gettext-perl (= 1.07-7+b2), liblsan0 (= 15.2.0-1), libltdl-dev (= 2.5.4-4), libltdl7 (= 2.5.4-4), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.1-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libmunge2 (= 0.5.16-1), libncurses6 (= 6.5+20250216-2), libnettle8t64 (= 3.10.1-1), libnghttp2-14 (= 1.64.0-1.1+b1), libnghttp3-9 (= 1.8.0-1), libngtcp2-16 (= 1.11.0-1), libngtcp2-crypto-gnutls8 (= 1.11.0-1), libnl-3-200 (= 3.7.0-2), libnl-3-dev (= 3.7.0-2), libnl-route-3-200 (= 3.7.0-2), libnl-route-3-dev (= 3.7.0-2), libnuma-dev (= 2.0.19-1), libnuma1 (= 2.0.19-1), libopenmpi-dev (= 5.0.7-1), libopenmpi40 (= 5.0.7-1), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpciaccess0 (= 0.17-3+b3), libpcre2-8-0 (= 10.45-1), libperl5.42 (= 5.42.0-1), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libpmix-dev (= 6.0.0-2), libpmix2t64 (= 6.0.0-2), libpsl5t64 (= 0.21.2-1.1+b1), libpsm2-2 (= 11.2.185-2.1), libquadmath0 (= 15.2.0-1), librdmacm1t64 (= 56.1-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-3), libsasl2-2 (= 2.1.28+dfsg1-9), libsasl2-modules-db (= 2.1.28+dfsg1-9), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsemanage-common (= 3.8.1-1), libsemanage2 (= 3.8.1-1), libsepol2 (= 3.8.1-1), libsframe2 (= 2.45-4), libsmartcols1 (= 2.41.1-1), libsparsehash-dev (= 2.0.3-2), libsqlite3-0 (= 3.46.1-7), libsqlite3-dev (= 3.46.1-7), libssh2-1t64 (= 1.11.1-1), libssl3t64 (= 3.5.2-1), libstdc++-14-dev (= 14.3.0-5), libstdc++6 (= 15.2.0-1), libsystemd0 (= 258~rc2-2), libtasn1-6 (= 4.20.0-2), libtext-markdown-perl (= 1.000031-5), libtext-multimarkdown-perl (= 1.000035-3), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 15.2.0-1), libubsan1 (= 15.2.0-1), libuchardet0 (= 0.0.8-1+b2), libucx0 (= 1.18.1+ds-2+b1), libudev1 (= 258~rc2-2), libunistring5 (= 1.3-2), liburi-perl (= 5.30-1), libuuid1 (= 2.41.1-1), libx11-6 (= 2:1.8.12-1), libx11-data (= 2:1.8.12-1), libxau6 (= 1:1.0.11-1), libxcb1 (= 1.17.0-2+b1), libxdmcp6 (= 1:1.1.5-1), libxext6 (= 2:1.3.4-1+b3), libxml2 (= 2.12.7+dfsg+really2.9.14-2.1), libxml2-16 (= 2.14.5+dfsg-0.1), libxnvctrl0 (= 535.171.04-1+b2), libz3-4 (= 4.13.3-1), libze1 (= 1.24.1-2), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.38-1), login.defs (= 1:4.17.4-2), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), ocl-icd-libopencl1 (= 2.3.3-1), openmpi-bin (= 5.0.7-1), openmpi-common (= 5.0.7-1), openssh-client (= 1:10.0p1-8), openssl-provider-legacy (= 3.5.2-1), passwd (= 1:4.17.4-2), patch (= 2.8-2), perl (= 5.42.0-1), perl-base (= 5.42.0-1), perl-modules-5.42 (= 5.42.0-1), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), samtools (= 1.21-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.1-1), wget (= 1.25.0-2), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1730552442" +------------------------------------------------------------------------------+ | Package contents Sun, 17 Aug 2025 06:29:59 +0000 | +------------------------------------------------------------------------------+ abyss-dbgsym_2.3.10-1_amd64.deb ------------------------------- new Debian package, version 2.0. size 30455224 bytes: control archive=2520 bytes. 2088 bytes, 12 lines control 4640 bytes, 44 lines md5sums Package: abyss-dbgsym Source: abyss Version: 2.3.10-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 32958 Depends: abyss (= 2.3.10-1) Section: debug Priority: optional Description: debug symbols for abyss Build-Ids: 07897af2a5d5326e12ccf46e8652a313b96137e0 0c485a20d3ad04a33863b3e589dd085b19808004 11b2996b8b67920bf471f6894b2119f4a29260d5 1b840f13dde97b9328141aa34e536e31fe68de71 1ec9bca636d0e99b7517bf80f441e0be9289a0af 2067cd0039edb1f24c86748bbd6b8640a2cd4263 236f351afbc8abc3a55d3bc5d31319b23442424d 267f8effade52a5afd0f6e9f3d9b16d161da3492 2b367906e228bf92ab01dadd1e7c5ffd71f0f175 31a01614630b0df3cc09ab15b1bfd347c2e54741 550161d1b64e7d781054e22d513d5f962a0d55f2 564c4f1132be12afce016e76cf03cf528f38de46 56b3f39af65dda097a4fb3cde63420cf3a6f690c 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root/root 0 2024-11-02 13:00 ./usr/share/doc/abyss-dbgsym -> abyss abyss_2.3.10-1_amd64.deb ------------------------ new Debian package, version 2.0. size 3340300 bytes: control archive=2672 bytes. 710 bytes, 14 lines control 4847 bytes, 77 lines md5sums Package: abyss Version: 2.3.10-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 10084 Depends: make, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi40 (>= 5.0.7), 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 2024-11-02 13:00 ./ drwxr-xr-x root/root 0 2024-11-02 13:00 ./usr/ drwxr-xr-x root/root 0 2024-11-02 13:00 ./usr/bin/ -rwxr-xr-x root/root 145840 2024-11-02 13:00 ./usr/bin/DistanceEst -rwxr-xr-x root/root 134192 2024-11-02 13:00 ./usr/bin/abyss-fixmate -rwxr-xr-x root/root 23209 2024-11-02 13:00 ./usr/bin/abyss-pe drwxr-xr-x root/root 0 2024-11-02 13:00 ./usr/lib/ drwxr-xr-x root/root 0 2024-11-02 13:00 ./usr/lib/abyss/ -rwxr-xr-x root/root 276928 2024-11-02 13:00 ./usr/lib/abyss/ABYSS -rwxr-xr-x root/root 321984 2024-11-02 13:00 ./usr/lib/abyss/ABYSS-P -rwxr-xr-x root/root 182696 2024-11-02 13:00 ./usr/lib/abyss/AdjList -rwxr-xr-x root/root 84384 2024-11-02 13:00 ./usr/lib/abyss/Consensus -rwxr-xr-x root/root 108976 2024-11-02 13:00 ./usr/lib/abyss/DAssembler -rwxr-xr-x root/root 145840 2024-11-02 13:00 ./usr/lib/abyss/DistanceEst -rwxr-xr-x root/root 145840 2024-11-02 13:00 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root/root 1135 2024-11-02 13:00 ./usr/lib/abyss/abyss-bowtie -rwxr-xr-x root/root 1192 2024-11-02 13:00 ./usr/lib/abyss/abyss-bowtie2 -rwxr-xr-x root/root 1208 2024-11-02 13:00 ./usr/lib/abyss/abyss-bwa -rwxr-xr-x root/root 1454 2024-11-02 13:00 ./usr/lib/abyss/abyss-bwamem -rwxr-xr-x root/root 1362 2024-11-02 13:00 ./usr/lib/abyss/abyss-bwasw -rwxr-xr-x root/root 67984 2024-11-02 13:00 ./usr/lib/abyss/abyss-db-csv -rwxr-xr-x root/root 703 2024-11-02 13:00 ./usr/lib/abyss/abyss-db-txt -rwxr-xr-x root/root 2739 2024-11-02 13:00 ./usr/lib/abyss/abyss-dida -rwxr-xr-x root/root 84392 2024-11-02 13:00 ./usr/lib/abyss/abyss-fac -rwxr-xr-x root/root 2058 2024-11-02 13:00 ./usr/lib/abyss/abyss-fatoagp -rwxr-xr-x root/root 174512 2024-11-02 13:00 ./usr/lib/abyss/abyss-filtergraph -rwxr-xr-x root/root 134192 2024-11-02 13:00 ./usr/lib/abyss/abyss-fixmate -rwxr-xr-x root/root 134192 2024-11-02 13:00 ./usr/lib/abyss/abyss-fixmate-ssq -rwxr-xr-x root/root 104880 2024-11-02 13:00 ./usr/lib/abyss/abyss-gapfill -rwxr-xr-x root/root 88464 2024-11-02 13:00 ./usr/lib/abyss/abyss-gc -rwxr-xr-x root/root 92568 2024-11-02 13:00 ./usr/lib/abyss/abyss-index -rwxr-xr-x root/root 108952 2024-11-02 13:00 ./usr/lib/abyss/abyss-junction -rwxr-xr-x root/root 39 2024-11-02 13:00 ./usr/lib/abyss/abyss-kaligner -rwxr-xr-x root/root 129432 2024-11-02 13:00 ./usr/lib/abyss/abyss-layout -rwxr-xr-x root/root 104864 2024-11-02 13:00 ./usr/lib/abyss/abyss-longseqdist -rwxr-xr-x root/root 182696 2024-11-02 13:00 ./usr/lib/abyss/abyss-map -rwxr-xr-x root/root 190888 2024-11-02 13:00 ./usr/lib/abyss/abyss-map-ssq -rwxr-xr-x root/root 84408 2024-11-02 13:00 ./usr/lib/abyss/abyss-mergepairs -rwxr-xr-x root/root 203192 2024-11-02 13:00 ./usr/lib/abyss/abyss-overlap -rwxr-xr-x root/root 285128 2024-11-02 13:00 ./usr/lib/abyss/abyss-paired-dbg -rwxr-xr-x root/root 330176 2024-11-02 13:00 ./usr/lib/abyss/abyss-paired-dbg-mpi -rwxr-xr-x root/root 23209 2024-11-02 13:00 ./usr/lib/abyss/abyss-pe 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./usr/share/doc/abyss/test-data/ -rw-r--r-- root/root 743013 2024-11-02 13:00 ./usr/share/doc/abyss/test-data/reads1.fastq.gz -rw-r--r-- root/root 743377 2024-11-02 13:00 ./usr/share/doc/abyss/test-data/reads2.fastq.gz drwxr-xr-x root/root 0 2024-11-02 13:00 ./usr/share/man/ drwxr-xr-x root/root 0 2024-11-02 13:00 ./usr/share/man/man1/ -rw-r--r-- root/root 1020 2024-11-02 13:00 ./usr/share/man/man1/DistanceEst.1.gz -rw-r--r-- root/root 790 2024-11-02 13:00 ./usr/share/man/man1/abyss-fixmate.1.gz -rw-r--r-- root/root 3562 2024-11-02 13:00 ./usr/share/man/man1/abyss-pe.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 17 Aug 2025 06:30:00 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 17 Aug 2025 06:30:00 +0000 | +------------------------------------------------------------------------------+ Purging /build/abyss-TAe4SE Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 17 Aug 2025 06:30:01 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 758936 Build-Time: 340 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 16 Job: /srv/debomatic/incoming/abyss_2.3.10-1.dsc Machine Architecture: amd64 Package: abyss Package-Time: 364 Source-Version: 2.3.10-1 Space: 758936 Status: successful Version: 2.3.10-1 -------------------------------------------------------------------------------- Finished at 2025-08-17T06:29:58Z Build needed 00:06:04, 758936k disk space