sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | abyss 2.3.10-3 (amd64) Sun, 18 Oct 2026 00:03:52 +0000 | +==============================================================================+ Package: abyss Version: 2.3.10-3 Source Version: 2.3.10-3 Distribution: perl-5.44-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, 18 Oct 2026 00:03:53 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup abyss_2.3.10-3 perl-5.44-throwaway amd64 --------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup abyss_2.3.10-3 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 18 Oct 2026 00:03:53 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.44 InRelease [3042 B] Hit:3 http://deb.debian.org/debian sid InRelease Get:4 file:/srv/reprepro perl-5.44/main amd64 Packages [612 kB] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Sun, 18 Oct 2026 00:03:55 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/abyss_2.3.10-3.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 18 Oct 2026 00:03:55 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 14), dh-sequence-single-binary, 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 (= 14), dh-sequence-single-binary, 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-Cm50Ye/resolver-5uqsiS/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/abyss-Cm50Ye/resolver-5uqsiS/apt_archive ./ InRelease Get:2 copy:/build/abyss-Cm50Ye/resolver-5uqsiS/apt_archive ./ Release [609 B] Ign:3 copy:/build/abyss-Cm50Ye/resolver-5uqsiS/apt_archive ./ Release.gpg Get:4 copy:/build/abyss-Cm50Ye/resolver-5uqsiS/apt_archive ./ Sources [804 B] Get:5 copy:/build/abyss-Cm50Ye/resolver-5uqsiS/apt_archive ./ Packages [834 B] Fetched 2247 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: architecture-properties autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file fonts-font-awesome fonts-font-awesome-legacy fonts-lato gettext gettext-base gfortran-16 gfortran-16-x86-64-linux-gnu groff-base help2man ibverbs-providers intltool-debian libamd-comgr3 libamdhip64-6 libarchive-zip-perl libboost-atomic1.92-dev libboost-atomic1.92.0 libboost-chrono1.92-dev libboost-chrono1.92.0 libboost-container1.92-dev libboost-container1.92.0 libboost-date-time1.92-dev libboost-date-time1.92.0 libboost-exception1.92-dev libboost-graph-dev libboost-graph1.92-dev libboost-graph1.92.0 libboost-math1.92-dev libboost-math1.92.0 libboost-random1.92-dev libboost-random1.92.0 libboost-regex1.92-dev libboost-regex1.92.0 libboost-serialization1.92-dev libboost-serialization1.92.0 libboost-test1.92-dev libboost-test1.92.0 libboost-thread1.92-dev libboost-thread1.92.0 libboost1.92-dev libbrotli1 libbsd0 libbtllib-dev libcbor0.10 libclang-common-21-dev libcom-err2 libcpptoml-dev libcurl4-gnutls libdebhelper-perl libdeflate0 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libesmtp6 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 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libfuse3-4 libgfortran-16-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhtml-parser-perl libhtml-tagset-perl libhts3t64 libhtscodecs2 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm21 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libpciaccess0 libpipeline1 libpkgconf7 libpmix2t64 libprrte-bin libprrte-dev libprrte4 libpsl5t64 libpsm2-2 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib librdmacm1t64 libsparsehash-dev libsqlite3-dev libssh2-1t64 libsystemd-shared libtext-markdown-perl libtext-multimarkdown-perl libtool libucc1 libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2-16 libxnvctrl0 libz3-4 libze1 m4 man-db media-types netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssh-common pci.ids pkgconf pkgconf-bin po-debconf prrte-common python3 python3-minimal python3.14 python3.14-minimal samtools sensible-utils systemd tzdata wget zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make node-fortawesome-fontawesome-free gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n gfortran-16-multilib gfortran-16-doc libcoarrays-dev groff graphviz libboost1.92-doc libboost-cobalt1.92-dev libboost-context1.92-dev libboost-contract1.92-dev libboost-coroutine1.92-dev libboost-fiber1.92-dev libboost-filesystem1.92-dev libboost-graph-parallel1.92-dev libboost-iostreams1.92-dev libboost-json1.92-dev libboost-locale1.92-dev libboost-log1.92-dev libboost-mpi-python1.92-dev libboost-mpi1.92-dev libboost-nowide1.92-dev libboost-numpy1.92-dev libboost-program-options1.92-dev libboost-python1.92-dev libboost-stacktrace1.92-dev libboost-timer1.92-dev libboost-type-erasure1.92-dev libboost-url1.92-dev libboost-wave1.92-dev libboost1.92-tools-dev libmpfrc++-dev libntl-dev fuse3 krb5-doc krb5-user libdata-dump-perl libhwloc-contrib-plugins libjs-jquery-ui-docs libtool-doc openmpi-doc sqlite3-doc libapparmor1 libarchive13t64 libbpf1 libcryptsetup12 libcurl4t64 libdw1t64 libfdisk1 libkmod2 libmicrohttpd12t64 libpwquality1 libqrencode4 libtss2-esys-3.0.2-0t64 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 python3-doc python3-tk python3-venv python3.14-venv python3.14-doc binfmt-support cwltool systemd-container systemd-homed systemd-imds systemd-userdbd systemd-boot systemd-report systemd-resolved systemd-repart polkitd Recommended packages: python3-requests libsdsl-dev libclang-rt-21-dev ca-certificates libarchive-cpio-perl libhttp-message-perl javascript-common krb5-locales libgpm2 libcoarrays-openmpi-dev libpmix-dev publicsuffix xauth libmail-sendmail-perl default-dbus-system-bus | dbus-system-bus linux-sysctl-defaults login systemd-timesyncd | time-daemon systemd-tpm systemd-cryptsetup libapparmor1 libbpf1 libcryptsetup12 libkmod2 The following NEW packages will be installed: architecture-properties autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file fonts-font-awesome fonts-font-awesome-legacy fonts-lato gettext gettext-base gfortran-16 gfortran-16-x86-64-linux-gnu groff-base help2man ibverbs-providers intltool-debian libamd-comgr3 libamdhip64-6 libarchive-zip-perl libboost-atomic1.92-dev libboost-atomic1.92.0 libboost-chrono1.92-dev libboost-chrono1.92.0 libboost-container1.92-dev libboost-container1.92.0 libboost-date-time1.92-dev libboost-date-time1.92.0 libboost-exception1.92-dev libboost-graph-dev libboost-graph1.92-dev libboost-graph1.92.0 libboost-math1.92-dev libboost-math1.92.0 libboost-random1.92-dev libboost-random1.92.0 libboost-regex1.92-dev libboost-regex1.92.0 libboost-serialization1.92-dev libboost-serialization1.92.0 libboost-test1.92-dev libboost-test1.92.0 libboost-thread1.92-dev libboost-thread1.92.0 libboost1.92-dev libbrotli1 libbsd0 libbtllib-dev libcbor0.10 libclang-common-21-dev libcom-err2 libcpptoml-dev libcurl4-gnutls libdebhelper-perl libdeflate0 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 libesmtp6 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 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libfuse3-4 libgfortran-16-dev libgfortran5 libgssapi-krb5-2 libhsa-runtime64-1 libhtml-parser-perl libhtml-tagset-perl libhts3t64 libhtscodecs2 libhwloc-dev libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs-dev libibverbs1 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libllvm21 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi40 libpciaccess0 libpipeline1 libpkgconf7 libpmix2t64 libprrte-bin libprrte-dev libprrte4 libpsl5t64 libpsm2-2 libpython3-stdlib libpython3.14-minimal libpython3.14-stdlib librdmacm1t64 libsparsehash-dev libsqlite3-dev libssh2-1t64 libsystemd-shared libtext-markdown-perl libtext-multimarkdown-perl libtool libucc1 libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2-16 libxnvctrl0 libz3-4 libze1 m4 man-db media-types netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client openssh-common pci.ids pkgconf pkgconf-bin po-debconf prrte-common python3 python3-minimal python3.14 python3.14-minimal samtools sbuild-build-depends-main-dummy sensible-utils systemd tzdata wget zlib1g-dev 0 upgraded, 176 newly installed, 0 to remove and 0 not upgraded. Need to get 157 MB/157 MB of archives. After this operation, 788 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.44/main amd64 liblocale-gettext-perl amd64 1.07-10+b2 [14.9 kB] Get:2 copy:/build/abyss-Cm50Ye/resolver-5uqsiS/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [960 B] Get:3 file:/srv/reprepro perl-5.44/main amd64 libhtml-parser-perl amd64 3.83-2+b3 [100.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 262.1-1 [2792 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 systemd amd64 262.1-1 [3477 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.9.0-1 [133 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libpython3.14-minimal amd64 3.14.8-1 [902 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 python3.14-minimal amd64 3.14.8-1 [2715 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.14.7-3 [25.3 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 netbase all 6.6 [10.3 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 tzdata all 2026e-1 [262 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libpython3.14-stdlib amd64 3.14.8-1 [2367 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 python3.14 amd64 3.14.8-1 [874 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.14.7-3 [8252 B] Get:17 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.14.7-3 [26.0 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-5 [334 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.2-2 [1365 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.4-1 [103 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2.2 [29.0 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.17.0-2 [80.5 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 openssh-common amd64 1:10.6p1-1 [505 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-3 [132 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20260512-1 [93.6 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:10.6p1-1 [735 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.23.3-1 [61.7 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 wget amd64 1.25.0-3 [985 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6+b2 [2632 B] Get:37 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.19-2 [891 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-5 [820 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.5 [77.7 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libtool all 2.6.2-3 [552 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 23 [12.7 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:48 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.196-1 [61.2 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.17-1 [109 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.4+dfsg-1 [683 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-5 [2704 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.5 [944 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome-legacy all 6-4 [1547 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 7.3.0+dfsg-1 [677 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 16.2.0-3 [879 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgfortran-16-dev amd64 16.2.0-3 [921 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 gfortran-16-x86-64-linux-gnu amd64 16.2.0-3 [14.5 MB] Get:60 http://deb.debian.org/debian unstable/main amd64 gfortran-16 amd64 16.2.0-3 [16.5 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.12.0-2+b1 [62.2 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.12.0-2+b1 [200 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 65.0-1.1 [68.2 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 65.0-1.1 [424 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1.1 [8644 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-13 [28.3 MB] Get:68 http://deb.debian.org/debian unstable/main amd64 libclang-common-21-dev amd64 1:21.1.8-13 [769 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libamd-comgr3 amd64 7.0.2+dfsg-3 [13.9 MB] Get:70 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.134-3 [7860 B] Get:71 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.134-3 [38.5 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.134-3 [23.3 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.19-1+b2 [22.0 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.4.3+dfsg-5 [678 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libamdhip64-6 amd64 6.4.3-5 [9385 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.92.0 amd64 1.92.0-4 [320 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.92-dev amd64 1.92.0-4 [339 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libboost1.92-dev amd64 1.92.0-4 [11.6 MB] Get:79 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.92.0 amd64 1.92.0-4 [228 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.92-dev amd64 1.92.0-4 [231 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.92.0 amd64 1.92.0-4 [239 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.92-dev amd64 1.92.0-4 [246 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libboost-container1.92.0 amd64 1.92.0-4 [253 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libboost-container1.92-dev amd64 1.92.0-4 [259 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libboost-exception1.92-dev amd64 1.92.0-4 [225 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.92.0 amd64 1.92.0-4 [223 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.92.0 amd64 1.92.0-4 [261 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.92-dev amd64 1.92.0-4 [270 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.92.0 amd64 1.92.0-4 [336 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.92-dev amd64 1.92.0-4 [381 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.92-dev amd64 1.92.0-4 [234 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libboost-random1.92.0 amd64 1.92.0-4 [238 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libboost-random1.92-dev amd64 1.92.0-4 [241 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libboost-math1.92.0 amd64 1.92.0-4 [476 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libboost-math1.92-dev amd64 1.92.0-4 [520 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.92.0 amd64 1.92.0-4 [362 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libboost-test1.92.0 amd64 1.92.0-4 [465 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libboost-test1.92-dev amd64 1.92.0-4 [558 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.92-dev amd64 1.92.0-4 [394 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libboost-graph-dev amd64 1.92.0.1 [3156 B] Get:101 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-4+b1 [312 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libcpptoml-dev all 0.1.1-3 [180 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.17.0-1 [68.1 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.24.0-1 [145 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:106 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1+b2 [19.5 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:109 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.70.0-1 [92.7 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.24.0-1 [23.9 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-6 [253 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.23.0-1 [463 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.7-1 [102 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.24-3 [506 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.6+20260608-2 [107 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.24-2 [730 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 libbtllib-dev amd64 1.7.5+dfsg-2 [218 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 libesmtp6 amd64 1.1.0-3.2+b2 [59.3 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.13-stable-1 [183 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.13-stable-1 [133 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.13-stable-1 [108 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.13-stable-1 [53.8 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.13-stable-1 [60.9 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.13-stable-1 [307 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 65.0-1.1 [79.2 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 2.1.0-1.1+b2 [716 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 libfuse3-4 amd64 3.18.3-1 [109 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.37-1 [113 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.15.0-2 [178 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.19-1+b2 [36.2 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.6.2-3 [427 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.6.2-3 [171 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.15.0-2 [273 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 pci.ids all 0.0~2026.09.23-1 [287 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.19-2 [18.5 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b2 [20.7 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2+b1 [28.2 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.13-1 [346 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.13-1 [829 kB] Get:146 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b3 [14.1 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 libze1 amd64 1.32.0-1 [648 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.4-1+b1 [42.8 kB] Get:150 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.15.0-2 [22.4 kB] Get:151 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 65.0-1.1 [29.8 kB] Get:152 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 65.0-1.1 [44.3 kB] Get:153 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.12.0-2+b1 [105 kB] Get:154 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.12.0-2+b1 [220 kB] Get:155 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 65.0-1.1 [759 kB] Get:156 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1 [319 kB] Get:157 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.14.2+dfsg-1 [245 kB] Get:158 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 7.0.0~rc1-2 [839 kB] Get:159 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.22.0-2 [1027 kB] Get:160 http://deb.debian.org/debian unstable/main amd64 libucc1 amd64 1.9.0-1 [379 kB] Get:161 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 6.0.0~rc2-2 [2880 kB] Get:162 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 6.0.0~rc2-2 [15.8 kB] Get:163 http://deb.debian.org/debian unstable/main amd64 libprrte4 amd64 5.0.0~rc1-1 [725 kB] Get:164 http://deb.debian.org/debian unstable/main amd64 prrte-common all 5.0.0~rc1-1 [60.1 kB] Get:165 http://deb.debian.org/debian unstable/main amd64 libprrte-dev amd64 5.0.0~rc1-1 [4328 kB] Get:166 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:167 http://deb.debian.org/debian unstable/main amd64 libprrte-bin amd64 5.0.0~rc1-1 [115 kB] Get:168 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 6.0.0~rc2-2 [172 kB] Get:169 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 6.0.0~rc2-2 [1224 kB] Get:170 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Get:171 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.4-2 [76.8 kB] Get:172 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.53.4-2 [1166 kB] Get:173 http://deb.debian.org/debian unstable/main amd64 libtext-markdown-perl all 1.000031-5 [31.4 kB] Get:174 http://deb.debian.org/debian unstable/main amd64 libtext-multimarkdown-perl all 1.000035-3 [28.5 kB] Get:175 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Get:176 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Preconfiguring packages ... Fetched 157 MB in 1s (141 MB/s) Selecting previously unselected package libsystemd-shared:amd64. (Reading database ... 15717 files and directories currently installed.) Preparing to unpack .../libsystemd-shared_262.1-1_amd64.deb ... Unpacking libsystemd-shared:amd64 (262.1-1) ... Setting up libsystemd-shared:amd64 (262.1-1) ... Selecting previously unselected package systemd. (Reading database ... 15725 files and directories currently installed.) Preparing to unpack .../0-systemd_262.1-1_amd64.deb ... Unpacking systemd (262.1-1) ... Selecting previously unselected package fonts-lato. Preparing to unpack .../1-fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../2-libexpat1_2.9.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.9.0-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../3-liblocale-gettext-perl_1.07-10+b2_amd64.deb ... 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Setting up libpython3-stdlib:amd64 (3.14.7-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.134-3) ... Setting up libcurl4-gnutls:amd64 (8.23.0-1) ... Setting up libibverbs1:amd64 (65.0-1.1) ... Creating group 'rdma' with GID 993. Setting up ibverbs-providers:amd64 (65.0-1.1) ... Setting up openssh-client (1:10.6p1-1) ... Created symlink '/etc/systemd/user/sockets.target.wants/ssh-agent.socket' → '/usr/lib/systemd/user/ssh-agent.socket'. Setting up po-debconf (1.0.22) ... Setting up python3 (3.14.7-3) ... Setting up libhwloc-plugins:amd64 (2.15.0-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'. Setting up libnl-route-3-dev:amd64 (3.12.0-2+b1) ... Setting up libevent-dev (2.1.13-stable-1) ... Setting up libpmix2t64:amd64 (7.0.0~rc1-2) ... Setting up libhsa-runtime64-1:amd64 (6.4.3+dfsg-5) ... Setting up libhts3t64:amd64 (1.24-3) ... 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Setting up openmpi-bin (6.0.0~rc2-2) ... 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/mpirun.1.gz because associated file /usr/share/man/man1/mpirun.openmpi.1.gz (of link group mpirun) does not exist update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) does not exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpicc.1.gz because associated file /usr/share/man/man1/mpicc.openmpi.1.gz (of link group mpi) does not exist update-alternatives: warning: skip creation of /usr/share/man/man1/mpic++.1.gz because associated file /usr/share/man/man1/mpic++.openmpi.1.gz (of link group mpi) does not exist update-alternatives: warning: skip creation of /usr/share/man/man1/mpicxx.1.gz because associated file /usr/share/man/man1/mpicxx.openmpi.1.gz (of link group mpi) does not exist update-alternatives: warning: skip creation of /usr/share/man/man1/mpiCC.1.gz because associated file /usr/share/man/man1/mpiCC.openmpi.1.gz (of link group mpi) does not exist update-alternatives: warning: skip creation of /usr/share/man/man1/mpif77.1.gz because associated file /usr/share/man/man1/mpif77.openmpi.1.gz (of link group mpi) does not exist update-alternatives: warning: skip creation of /usr/share/man/man1/mpif90.1.gz because associated file /usr/share/man/man1/mpif90.openmpi.1.gz (of link group mpi) does not exist update-alternatives: warning: skip creation of /usr/share/man/man1/mpifort.1.gz because associated file /usr/share/man/man1/mpifort.openmpi.1.gz (of link group mpi) does not exist Setting up libopenmpi-dev (6.0.0~rc2-2) ... 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 libboost1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-random1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-exception1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-atomic1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-regex1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-chrono1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-test1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-container1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-date-time1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-thread1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-math1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-serialization1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-graph1.92-dev:amd64 (1.92.0-4) ... Setting up libboost-graph-dev:amd64 (1.92.0.1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.43-7) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 18 Oct 2026 00:04:19 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sun, 18 Oct 2026 00:04:19 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.47-6 dpkg-dev_1.23.11 g++-15_15.3.0-4 g++-16_16.2.0-3 gcc-15_15.3.0-4 gcc-16_16.2.0-3 libc6-dev_2.43-7 libstdc++-15-dev_15.3.0-4 libstdc++-16-dev_16.2.0-3 libstdc++6_16.2.0-3 linux-libc-dev_7.2.11-1 Package versions: apt_3.3.3 architecture-properties_0.2.6+b2 autoconf_2.73-2 automake_1:1.19-2 autopoint_1.0-5 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-4 binutils_2.47-6 binutils-common_2.47-6 binutils-x86-64-linux-gnu_2.47-6 bsdextrautils_2.42.4-1 build-essential_12.12 bzip2_1.0.8-6+b2 coreutils_9.10-1 cpp_4:16.1.0-3 cpp-15_15.3.0-4 cpp-15-x86-64-linux-gnu_15.3.0-4 cpp-16_16.2.0-3 cpp-16-x86-64-linux-gnu_16.2.0-3 cpp-x86-64-linux-gnu_4:16.1.0-3 dash_0.5.12-12 debconf_1.5.92 debhelper_14.5 debian-archive-keyring_2025.1 debianutils_5.24 dh-autoreconf_23 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-8 dpkg_1.23.11 dpkg-dev_1.23.11 dwz_0.17-1 eatmydata_131-2 file_1:5.47-4 findutils_4.11.0-3 fonts-font-awesome_7.3.0+dfsg-1 fonts-font-awesome-legacy_6-4 fonts-lato_2.015-1 g++_4:16.1.0-3 g++-15_15.3.0-4 g++-15-x86-64-linux-gnu_15.3.0-4 g++-16_16.2.0-3 g++-16-x86-64-linux-gnu_16.2.0-3 g++-x86-64-linux-gnu_4:16.1.0-3 gcc_4:16.1.0-3 gcc-15_15.3.0-4 gcc-15-base_15.3.0-4 gcc-15-x86-64-linux-gnu_15.3.0-4 gcc-16_16.2.0-3 gcc-16-base_16.2.0-3 gcc-16-x86-64-linux-gnu_16.2.0-3 gcc-x86-64-linux-gnu_4:16.1.0-3 gettext_1.0-5 gettext-base_1.0-5 gfortran-16_16.2.0-3 gfortran-16-x86-64-linux-gnu_16.2.0-3 gnupg_2.4.9-8 gnupg-l10n_2.4.9-8 gpg_2.4.9-8 gpg-agent_2.4.9-8 gpgconf_2.4.9-8 gpgsm_2.4.9-8 grep_3.12-1 groff-base_1.24.2-2 gzip_1.14-1 help2man_1.49.3 hostname_3.25 ibverbs-providers_65.0-1.1 init-system-helpers_1.69+nmu3 intltool-debian_0.35.0+20060710.6 libacl1_2.4.0-1 libamd-comgr3_7.0.2+dfsg-3 libamdhip64-6_6.4.3-5 libapt-pkg7.0_3.3.3 libarchive-zip-perl_1.68-1 libasan8_16.2.0-3 libassuan9_3.0.2-2+b2 libatomic1_16.2.0-3 libattr1_1:2.6.0-1 libaudit-common_1:4.2.1-1 libaudit1_1:4.2.1-1 libbinutils_2.47-6 libblkid1_2.42.4-1 libboost-atomic1.92-dev_1.92.0-4 libboost-atomic1.92.0_1.92.0-4 libboost-chrono1.92-dev_1.92.0-4 libboost-chrono1.92.0_1.92.0-4 libboost-container1.92-dev_1.92.0-4 libboost-container1.92.0_1.92.0-4 libboost-date-time1.92-dev_1.92.0-4 libboost-date-time1.92.0_1.92.0-4 libboost-exception1.92-dev_1.92.0-4 libboost-graph-dev_1.92.0.1 libboost-graph1.92-dev_1.92.0-4 libboost-graph1.92.0_1.92.0-4 libboost-math1.92-dev_1.92.0-4 libboost-math1.92.0_1.92.0-4 libboost-random1.92-dev_1.92.0-4 libboost-random1.92.0_1.92.0-4 libboost-regex1.92-dev_1.92.0-4 libboost-regex1.92.0_1.92.0-4 libboost-serialization1.92-dev_1.92.0-4 libboost-serialization1.92.0_1.92.0-4 libboost-test1.92-dev_1.92.0-4 libboost-test1.92.0_1.92.0-4 libboost-thread1.92-dev_1.92.0-4 libboost-thread1.92.0_1.92.0-4 libboost1.92-dev_1.92.0-4 libbrotli1_1.2.0-4+b1 libbsd0_0.12.2-3 libbtllib-dev_1.7.5+dfsg-2 libbz2-1.0_1.0.8-6+b2 libc-bin_2.43-7 libc-dev-bin_2.43-7 libc-gconv-modules-extra_2.43-7 libc6_2.43-7 libc6-dev_2.43-7 libcap-ng0_0.9.6-1 libcbor0.10_0.10.2-2.2 libcc1-0_16.2.0-3 libclang-common-21-dev_1:21.1.8-13 libcom-err2_1.47.4-1+b2 libcpptoml-dev_0.1.1-3 libcrypt1_1:4.5.2+20251210-1 libctf-nobfd0_2.47-6 libctf0_2.47-6 libcurl4-gnutls_8.23.0-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.5 libdeflate0_1.25-1 libdpkg-perl_1.23.11 libdrm-amdgpu1_2.4.134-3 libdrm-common_2.4.134-3 libdrm2_2.4.134-3 libeatmydata1_131-2+b2 libedit2_3.1-20260512-1 libelf1t64_0.196-1 libesmtp6_1.1.0-3.2+b2 libevent-2.1-7t64_2.1.13-stable-1 libevent-core-2.1-7t64_2.1.13-stable-1 libevent-dev_2.1.13-stable-1 libevent-extra-2.1-7t64_2.1.13-stable-1 libevent-openssl-2.1-7t64_2.1.13-stable-1 libevent-pthreads-2.1-7t64_2.1.13-stable-1 libexpat1_2.9.0-1 libfabric1_2.1.0-1.1+b2 libffi8_3.8.0-2 libfido2-1_1.17.0-2 libfile-stripnondeterminism-perl_1.15.1-1 libfuse3-4_3.18.3-1 libgcc-15-dev_15.3.0-4 libgcc-16-dev_16.2.0-3 libgcc-s1_16.2.0-3 libgcrypt20_1.12.4-2 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgfortran-16-dev_16.2.0-3 libgfortran5_16.2.0-3 libgmp10_2:6.3.0+dfsg-5+b2 libgnutls30t64_3.8.13-1 libgomp1_16.2.0-3 libgpg-error0_1.61-5 libgprofng0_2.47-6 libgssapi-krb5-2_1.22.1-3 libhogweed6t64_3.10.2-1+b1 libhsa-runtime64-1_6.4.3+dfsg-5 libhtml-parser-perl_3.83-2+b3 libhtml-tagset-perl_3.24-1 libhts3t64_1.24-3 libhtscodecs2_1.6.7-1 libhwasan0_16.2.0-3 libhwloc-dev_2.15.0-2 libhwloc-plugins_2.15.0-2 libhwloc15_2.15.0-2 libibmad5_65.0-1.1 libibumad3_65.0-1.1 libibverbs-dev_65.0-1.1 libibverbs1_65.0-1.1 libidn2-0_2.3.8-5 libisl23_0.28-1 libitm1_16.2.0-3 libjansson4_2.15.1-1 libjs-jquery_3.7.1+dfsg+~3.5.33-1 libjs-jquery-ui_1.14.2+dfsg-1 libk5crypto3_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5support0_1.22.1-3 libksba8_1.8.1-1 libldap2_2.6.14+dfsg-2+b1 libllvm21_1:21.1.8-13 liblocale-gettext-perl_1.07-10+b2 liblsan0_16.2.0-3 libltdl-dev_2.6.2-3 libltdl7_2.6.2-3 liblz4-1_1.10.0-10 liblzma5_5.8.4-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.3.0-1 libmount1_2.42.4-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncurses6_6.6+20260608-2 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.70.0-1 libnghttp3-9_1.17.0-1 libngtcp2-16_1.24.0-1 libngtcp2-crypto-gnutls8_1.24.0-1 libnl-3-200_3.12.0-2+b1 libnl-3-dev_3.12.0-2+b1 libnl-route-3-200_3.12.0-2+b1 libnl-route-3-dev_3.12.0-2+b1 libnpth0t64_1.8-4 libnuma-dev_2.0.19-1+b2 libnuma1_2.0.19-1+b2 libopenmpi-dev_6.0.0~rc2-2 libopenmpi40_6.0.0~rc2-2 libp11-kit0_0.26.5-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpciaccess0_0.19-2 libpcre2-8-0_10.48-3.1 libperl5.40_5.40.1-8 libperl5.44_5.44.0-1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpmix2t64_7.0.0~rc1-2 libprrte-bin_5.0.0~rc1-1 libprrte-dev_5.0.0~rc1-1 libprrte4_5.0.0~rc1-1 libpsl5t64_0.23.3-1 libpsm2-2_11.2.185-2.1 libpython3-stdlib_3.14.7-3 libpython3.14-minimal_3.14.8-1 libpython3.14-stdlib_3.14.8-1 libquadmath0_16.2.0-3 librdmacm1t64_65.0-1.1 libreadline8t64_8.3-4 libsasl2-2_2.1.28+dfsg1-12 libsasl2-modules-db_2.1.28+dfsg1-12 libseccomp2_2.6.1-1+b1 libselinux1_3.11-2.1 libsframe3_2.47-6 libsmartcols1_2.42.4-1 libsparsehash-dev_2.0.4-2 libsqlite3-0_3.53.4-2 libsqlite3-dev_3.53.4-2 libssh2-1t64_1.11.1-6 libssl3t64_3.6.5-1 libstdc++-15-dev_15.3.0-4 libstdc++-16-dev_16.2.0-3 libstdc++6_16.2.0-3 libsystemd-shared_262.1-1 libsystemd0_262.1-1 libtasn1-6_4.21.0-2+b1 libtext-markdown-perl_1.000031-5 libtext-multimarkdown-perl_1.000035-3 libtinfo6_6.6+20260608-2 libtool_2.6.2-3 libtsan2_16.2.0-3 libtss2-mu-4.0.1-0t64_4.2.0-2 libtss2-rc0t64_4.2.0-2 libtss2-sys1t64_4.2.0-2 libtss2-tcti-device0t64_4.2.0-2 libtss2-tcti-mssim0t64_4.2.0-2 libtss2-tcti-swtpm0t64_4.2.0-2 libubsan1_16.2.0-3 libucc1_1.9.0-1 libuchardet0_0.0.8-2+b2 libucx0_1.22.0-2 libudev1_262.1-1 libunistring5_1.4.2-1 liburi-perl_5.37-1 libuuid1_2.42.4-1 libx11-6_2:1.8.13-1 libx11-data_2:1.8.13-1 libxau6_1:1.0.11-1+b2 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2+b1 libxext6_2:1.3.4-1+b4 libxml2-16_2.15.4+dfsg-1 libxnvctrl0_535.171.04-1+b3 libxxhash0_0.8.3-2+b2 libz3-4_4.13.3-1.1 libze1_1.32.0-1 libzstd1_1.5.7+dfsg-4 linux-libc-dev_7.2.11-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-2 media-types_14.0.0 mount_2.42.4-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 netbase_6.6 ocl-icd-libopencl1_2.3.4-1+b1 openmpi-bin_6.0.0~rc2-2 openmpi-common_6.0.0~rc2-2 openssh-client_1:10.6p1-1 openssh-common_1:10.6p1-1 openssl-provider-legacy_3.6.5-1 patch_2.8-2 pci.ids_0.0~2026.09.23-1 perl_5.44.0-1 perl-base_5.44.0-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0-1 pinentry-curses_1.3.3-3 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 prrte-common_5.0.0~rc1-1 python3_3.14.7-3 python3-minimal_3.14.7-3 python3.14_3.14.8-1 python3.14-minimal_3.14.8-1 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 samtools_1.24-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.5.0-1 systemd_262.1-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-6 tzdata_2026e-1 util-linux_2.42.4-1 wget_1.25.0-3 xz-utils_5.8.4-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Sun, 18 Oct 2026 00:04:19 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: abyss Binary: abyss Architecture: any Version: 2.3.10-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://github.com/bcgsc/abyss Standards-Version: 4.7.4 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 (= 14), dh-sequence-single-binary, 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 2b1ad8a31ee65295640f2b3202c6a371970756df 1499760 abyss_2.3.10-3.debian.tar.xz Checksums-Sha256: c8461eb017edfbd83c2aac9910da438df2d79660d2e87ab289f2de7a0d620a4c 933928 abyss_2.3.10.orig.tar.xz 9d90594502ffd6cf0884585deaf1ba24324ee7c231c5725e372c2dbc91430690 1499760 abyss_2.3.10-3.debian.tar.xz Files: b13b49e294474086d2e1395f5689843b 933928 abyss_2.3.10.orig.tar.xz 1a8417593eab3eb96d353ed7a8cf7a2e 1499760 abyss_2.3.10-3.debian.tar.xz Dgit: 19dbd917b5b02bed2b88504bf461551bb805bc3b debian archive/debian/2.3.10-3 https://git.dgit.debian.org/abyss -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmrTmZsUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoYZQ//QdP+SKBz2VbsNrS+s9VA1P5NdL59 lSaylXNrYqUu4pDLpafBWHAbq9wodEjhddFaZaLFb05pzOK95Onimg2V/ova5Rkm 1aBCJZG7Fe8/MRezU+g/9TLY6xnQhoZdJKocc6/gyC0sr3uc6+V3NoVB2efRy+6h /6O73Qd5EeZ2tquj73JTPa35zNnFzywX8e1+OW375Gx6rtqHi1px6jy0hZOrUEIU SvUy1b09YU5E9Z9tsajYYxRgvJTH9lYmf1JpijG7IImwODUtoQCUBtAgl+LQniGX v+CsFuu9G5Zpag3X3ylqMJnOnqsqG+7J7vnSzFMo45jhqjlBpBr/VeQHqNTMa+UE JqMBfeDgL4KYpnq7Rc/mFkIDyDuizwyy68qv89JFclPVWc4jFNKFt/8sFoWnQwjy qzwHfJYyzL8gdKGq2KiAQqJ4cijDgFSPM8ab1bD3IVJK40KT6xY4tPnCgPlYBwiv Rdonsfs1DTJRvtJEfE/G3RogFVEKDWgURzY0cEd4eYp9rvRz1rY7lYj2+HHa7mp3 x4f7W2SShaDOWOp0YnmAYKRxrBzzVlGtL2jhDtqNvFZ68C9Anw7d9nGp8GUPuLXA CdVGIwJ20hxJWRhAM7LbWV64MfJqRLvJsiNvz/YMo+yjwWz4x0rOH1gRM0/dd4V+ 02PDAqgqdATke6M= =NsLC -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./abyss_2.3.10-3.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./abyss_2.3.10-3.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting abyss in /build/abyss-Cm50Ye/abyss-2.3.10 dpkg-source: info: unpacking abyss_2.3.10.orig.tar.xz dpkg-source: info: unpacking abyss_2.3.10-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying fix-privacy-breach.patch dpkg-source: info: applying gcc-16.patch dpkg-source: info: applying mpi-libs.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Sun, 18 Oct 2026 00:04:20 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network abyss_2.3.10-3 perl-5.44-throwaway amd64 --------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network abyss_2.3.10-3 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/abyss-Cm50Ye/abyss-2.3.10 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-1b2d5434-89ce-4201-b99e-4d1827a784df 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 2.3.10-3 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_2.3.10-3.debian.tar.xz dpkg-source: info: building abyss in ../abyss_2.3.10-3.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: no obvious need to run autopoint autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: configure.ac: no need to run autopoint (confirmed) autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing configure.ac:25: installing './ar-lib' configure.ac:16: installing './compile' configure.ac:80: installing './config.guess' configure.ac:80: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' autoreconf: configure.ac: not running make: --make not given autoreconf: Leaving directory '.' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/abyss-Cm50Ye/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 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 x86_64-linux-gnu-g++ accepts -g... yes checking whether x86_64-linux-gnu-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 x86_64-linux-gnu-g++ -std=c++11... none checking for gawk... (cached) mawk checking for gcc... x86_64-linux-gnu-gcc checking whether the compiler supports GNU C... yes checking whether x86_64-linux-gnu-gcc accepts -g... yes checking for x86_64-linux-gnu-gcc option to enable C23 features... none needed checking whether x86_64-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-linux-gnu-gcc... none checking how to run the C preprocessor... x86_64-linux-gnu-gcc -E checking whether the compiler supports GNU C++... (cached) yes checking whether x86_64-linux-gnu-g++ -std=c++11 accepts -g... (cached) yes 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 whether malloc (0) returns nonnull... yes checking for working memcmp... yes checking whether realloc (0, 0) returns nonnull... yes checking for x86_64-linux-gnu-gcc options to detect undeclared functions... none needed checking for x86_64-linux-gnu-gcc options to ignore future-version 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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10' debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10' dh_auto_build make -j2 make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10' make all-recursive make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10' Making all in bin make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/bin' Making all in doc make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/doc' Making all in Common make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Common' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Common' Making all in Graph make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Graph' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc In file included from GraphIO.h:8, from todot.cc:9: DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ todot.cc:186:14: required from here 186 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ todot.cc:191:14: required from here 191 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Graph' Making all in DataLayer make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DataLayer' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DataBase' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/FMIndex' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/FMIndex' Making all in Assembly make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Assembly' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Assembly' Making all in dialign make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/dialign' x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o museq.o museq.c x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-Cm50Ye/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, | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-Cm50Ye/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, | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-Cm50Ye/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); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-Cm50Ye/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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o orf.o orf.c x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o parameters.o parameters.c x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o prob.o prob.c x86_64-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-Cm50Ye/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 x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/dialign' Making all in Align make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Align' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Align' Making all in ABYSS make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/ABYSS' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/ABYSS' Making all in Parallel make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Parallel' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopen_mpi -lmpi -ldl -lm x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopen_mpi -lmpi -ldl -lm make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Parallel' Making all in Bloom make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Bloom' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/BloomDBG' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Konnector' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Konnector' Making all in Consensus make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Consensus' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Consensus' Making all in DAssembler make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DAssembler' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DistanceEst' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/KAligner' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/KAligner' Making all in Layout make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Layout' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc In file included from ../Graph/GraphIO.h:8, from layout.cc:8: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ layout.cc:314:12: required from here 314 | write_dot(out, g); | ~~~~~~~~~^~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/LogKmerCount' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/LogKmerCount' Making all in Map make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Map' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc In file included from ../Graph/GraphIO.h:8, from overlap.cc:23: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ overlap.cc:502:13: required from here 502 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Map' Making all in MergePaths make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/MergePaths' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp In file included from ../Graph/GraphIO.h:8, from MergeContigs.cpp:13: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ MergeContigs.cpp:428:13: required from here 428 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/MergePaths' Making all in Overlap make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Overlap' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp Overlap.cpp: In function ‘int main(int, char**)’: Overlap.cpp:513:40: warning: possibly dangling reference to a temporary [-Wdangling-reference] 513 | const Overlap& ep = get(edge_bundle, scaffoldGraph, e); | ^~ Overlap.cpp:513:48: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 513 | const Overlap& ep = get(edge_bundle, scaffoldGraph, e); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../Graph/GraphIO.h:8, from Overlap.cpp:16: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Overlap; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ Overlap.cpp:481:35: required from here 481 | cout << dot_writer(scaffoldGraph); | ^ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Overlap.cpp:587:14: required from here 587 | write_graph(fout, graph, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PairedDBG' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/ParseAligns' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PathOverlap' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp In file included from ../Graph/GraphIO.h:8, from PathOverlap.cpp:10: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PathOverlap.cpp:709:14: required from here 709 | write_graph(out, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PopBubbles' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp In file included from ../Graph/GraphIO.h:8, from PopBubbles.cpp:16: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ PopBubbles.cpp:723:14: required from here 723 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Scaffold' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc In file included from ../Graph/GraphIO.h:8, from scaffold.cc:13: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ scaffold.cc:824:13: required from here 824 | write_dot(out, g); | ~~~~~~~~~^~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp In file included from ../Graph/GraphIO.h:8, from longseqdist.cpp:9: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = DistanceEst; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ longseqdist.cpp:208:11: required from here 208 | write_dot(cout, g); | ~~~~~~~~~^~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/SimpleGraph' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/kmerprint' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/FilterGraph' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc In file included from ../Graph/GraphIO.h:8, from FilterGraph.cc:15: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ FilterGraph.cc:825:14: required from here 825 | write_graph(fout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/GapFiller' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/GapFiller' Making all in Sealer make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Sealer' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Sealer' Making all in RResolver make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/RResolver' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp In file included from ../Graph/GraphIO.h:8, from Contigs.h:17, from Contigs.cpp:1: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Contigs.cpp:140:13: required from here 140 | write_graph(fout, g_contigGraph, program, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libralgorithmsshort_a-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp In file included from ../Graph/GraphIO.h:8, from Contigs.h:17, from Contigs.cpp:1: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ Contigs.cpp:140:13: required from here 140 | write_graph(fout, g_contigGraph, program, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/RResolver' Making all in AdjList make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/AdjList' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp In file included from ../Graph/GraphIO.h:8, from AdjList.cpp:15: ../Graph/DotIO.h: In instantiation of ‘void write_edges(std::ostream&, const Graph&, typename boost::graph_traits::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph >; EdgeProp = Distance; std::ostream = std::basic_ostream; typename boost::graph_traits::vertex_descriptor = ContigNode]’: ../Graph/DotIO.h:110:14: required from ‘std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 110 | write_edges(out, g, *u, (edge_property_type*)NULL); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:77:18: required from ‘std::ostream& write_dot(std::ostream&, const Graph&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream]’ 77 | return write_dot(out, g, "adj"); | ~~~~~~~~~^~~~~~~~~~~~~~~ ../Graph/DotIO.h:125:26: required from ‘std::ostream& operator<<(std::ostream&, const DotWriter > >&)’ 125 | return write_dot(out, o.g); | ~~~~~~~~~~~~~~~~^~~~~~~~~~ ../Graph/GraphIO.h:33:14: required from ‘std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph >; std::ostream = std::basic_ostream; std::string = std::__cxx11::basic_string]’ 33 | return out << dot_writer(g); | ~~~~^~~~~~~~~~~~~~~~ AdjList.cpp:401:13: required from here 401 | write_graph(cout, g, PROGRAM, commandLine); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference] 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ^~ ../Graph/DotIO.h:44:51: note: ‘ContigGraph >::out_edge_iterator’ {aka ‘DirectedGraph::out_edge_iterator’} temporary created here 44 | const edge_property_type& ep = get(edge_bundle, g, e); | ~~~^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/AdjList' Making all in vendor make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Unittest' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10' make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10' markdown README.md > README.html make[1]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10' dh_auto_test make -j2 check TESTSUITEFLAGS="-j2 --verbose" VERBOSE=1 make[1]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10' Making check in bin make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/bin' Making check in doc make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/doc' Making check in Common make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Common' Making check in Graph make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Graph' Making check in DataLayer make[2]: 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'/build/abyss-Cm50Ye/abyss-2.3.10/dialign' Making check in Align make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Align' Making check in ABYSS make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/ABYSS' Making check in Parallel make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Parallel' Making check in Bloom make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Bloom' Making check in BloomDBG make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/BloomDBG' Making check in Konnector make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Konnector' Making check in Consensus make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Consensus' Making check in DAssembler make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/KAligner' Making check in Layout make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/LogKmerCount' Making check in Map make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Map' Making check in MergePaths make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/MergePaths' Making check in Overlap make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Overlap' Making check in PairedDBG make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/GapFiller' Making check in Sealer make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Sealer' Making check in RResolver make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/RResolver' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/RResolver' Making check in AdjList make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/AdjList' Making check in vendor make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor' Making check in vendor/gtest-1.7.0 make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor/gtest-1.7.0' x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/vendor/gtest-1.7.0' make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/Unittest' x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-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-Cm50Ye/abyss-2.3.10 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-Cm50Ye/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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 x86_64-linux-gnu-g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-Cm50Ye/abyss-2.3.10=. -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-Cm50Ye/abyss-2.3.10/Unittest' make check-TESTS make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Unittest' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Unittest' PASS: common_histogram PASS: common_stringutil PASS: common_bitutil PASS: common_kmer PASS: common_sequence PASS: common_KmerIterator PASS: common_sam PASS: BloomFilter PASS: common_sam_ssq PASS: Konnector_DBGBloom PASS: Konnector_DBGBloomAlgorithms PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: graph_HashGraph PASS: graph_AllPathsSearch PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_ExtendPath PASS: graph_DotIO PASS: graph_UndirectedGraph PASS: Konnector_konnector PASS: PairedDBG_LoadAlgorithm PASS: PairedDBG_KmerPair PASS: DBG_LoadAlgorithm PASS: PairedDBG_Dinuc PASS: PairedDBG_BranchRecord PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer ============================================================================ Testsuite summary for ABySS 2.3.10 ============================================================================ # TOTAL: 34 # PASS: 34 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Unittest' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Unittest' make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Unittest' make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10' make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10' make[1]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10' dh_auto_install --destdir=debian/tmp make -j2 install DESTDIR=/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10' Making install in bin make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/bin' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/bin' /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /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-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/bin' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/bin' Making install in doc make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/doc' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/doc' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/doc' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/doc' Making install in Common make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Common' make[4]: Entering directory '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/Common' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Common' Making install in Graph make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Graph' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Graph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Graph' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Graph' Making install in DataLayer make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DataLayer' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DataLayer' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/DataLayer' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/DataLayer' Making install in DataBase make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DataBase' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DataBase' /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/DataBase' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/DataBase' Making install in FMIndex make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/FMIndex' make[4]: Entering directory '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/FMIndex' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/FMIndex' Making install in Assembly make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Assembly' make[4]: Entering directory '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/Assembly' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Assembly' Making install in dialign make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/dialign' make[4]: Entering directory '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/dialign' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/dialign' Making install in Align make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Align' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Align' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Align' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Align' Making install in ABYSS make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/ABYSS' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/ABYSS' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/ABYSS' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Parallel' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Parallel' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Parallel' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Parallel' Making install in Bloom make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Bloom' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Bloom' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Bloom' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/BloomDBG' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/BloomDBG' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Konnector' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Konnector' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Konnector' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Consensus' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Consensus' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Consensus' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DAssembler' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/DAssembler' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DistanceEst' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/DistanceEst' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/KAligner' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/KAligner' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/KAligner' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/KAligner' Making install in Layout make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Layout' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Layout' /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-layout '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Layout' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/LogKmerCount' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/LogKmerCount' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Map' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Map' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Map' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Map' Making install in MergePaths make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/MergePaths' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/MergePaths' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/MergePaths' Making install in Overlap make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Overlap' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Overlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Overlap' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PairedDBG' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/PairedDBG' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/ParseAligns' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/ParseAligns' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PathOverlap' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/PathOverlap' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PopBubbles' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/PopBubbles' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Scaffold' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Scaffold' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/SimpleGraph' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/SimpleGraph' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/kmerprint' make[4]: Entering directory '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/kmerprint' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/FilterGraph' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/FilterGraph' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/GapFiller' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/GapFiller' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/GapFiller' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/GapFiller' Making install in Sealer make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Sealer' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Sealer' /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Sealer' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Sealer' Making install in RResolver make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/RResolver' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/RResolver' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c abyss-rresolver-short '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/RResolver' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/RResolver' Making install in AdjList make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/AdjList' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/AdjList' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/AdjList' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/AdjList' Making install in vendor make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor' make[4]: Entering directory '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/vendor' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor/gtest-1.7.0' make[4]: Entering directory '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/vendor/gtest-1.7.0' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/vendor/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10/Unittest' make[4]: Entering directory '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/Unittest' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10/Unittest' make[3]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10' make[4]: Entering directory '/build/abyss-Cm50Ye/abyss-2.3.10' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10' make[3]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10' make[2]: Leaving directory '/build/abyss-Cm50Ye/abyss-2.3.10' chmod -R u\+rwX /build/abyss-Cm50Ye/abyss-2.3.10/debian/tmp 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-Cm50Ye/abyss-2.3.10' debian/rules override_dh_install make[1]: Entering directory '/build/abyss-Cm50Ye/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-Cm50Ye/abyss-2.3.10' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_missing 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_fixperms dh_strip_nondeterminism dh_compress dh_installdeb dh_computeautosubstvars dh_gencontrol dpkg-gencontrol: warning: Depends field of package abyss: substitution variable ${misc:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.10-3_amd64.deb'. dpkg-deb: building package 'abyss' in '../abyss_2.3.10-3_amd64.deb'. dpkg-genbuildinfo -O../abyss_2.3.10-3_amd64.buildinfo dpkg-genchanges -O../abyss_2.3.10-3_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2026-10-18T00:12:05Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 18 Oct 2026 00:12:05 +0000 | +------------------------------------------------------------------------------+ abyss_2.3.10-3_amd64.changes: ----------------------------- Format: 1.8 Date: Sat, 17 Oct 2026 17:43:32 +0200 Source: abyss Binary: abyss abyss-dbgsym Architecture: source amd64 Version: 2.3.10-3 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: abyss - de novo, parallel, sequence assembler for short reads Closes: 1150081 Changes: abyss (2.3.10-3) unstable; urgency=medium . * mpi-libs.patch: new: fix a link error against openmpi. (Closes: #1150081) * d/control: declare compliance to standards version 4.7.4. * d/control: bump to debhelper 14 in single-binary mode. Checksums-Sha1: 96b1162c3f5dac7aeb70fe27bb8c28b1d332504b 1313 abyss_2.3.10-3.dsc dceae3f668f6239e74ef1094a2c56ce658f2f5b4 1499768 abyss_2.3.10-3.debian.tar.xz 0742e82ab8cba3850e8592a9660388f032eb5fdd 38706116 abyss-dbgsym_2.3.10-3_amd64.deb 267c26c3d8258d9cf2bb9359bf0dd971e55ed6b7 10240 abyss_2.3.10-3_amd64.buildinfo a8019613122d30ff01eaed8cb5800e084e7ca44d 3400232 abyss_2.3.10-3_amd64.deb Checksums-Sha256: c39341f83f9cfa848fe1a888c4bbb84633076ca4bd247ba6ec540033ed0be866 1313 abyss_2.3.10-3.dsc 4bdf61fd49e7ad6e334d26056feb8bd52c918c1e2ddc92118601050e31b2328a 1499768 abyss_2.3.10-3.debian.tar.xz 314259a758c448f4f9d42e6b26ffef5d3e63153af8d4fbcd55160071b851d7ef 38706116 abyss-dbgsym_2.3.10-3_amd64.deb c99442773b5948abd627944321a1658d123dd7dc9bfa5e2ef63062f8af5535cc 10240 abyss_2.3.10-3_amd64.buildinfo d5e112b30af0aa96b49a38757831bba117910c16234d67e4d014333a5bdb6816 3400232 abyss_2.3.10-3_amd64.deb Files: f9c3f1b308f17e2c91d8ab47158de01b 1313 science optional abyss_2.3.10-3.dsc b6fdf033b94cca405ae96a1d3a352954 1499768 science optional abyss_2.3.10-3.debian.tar.xz 02390d5e2ce67a15f50b4381a785d5f4 38706116 debug optional abyss-dbgsym_2.3.10-3_amd64.deb 2c0ca082d1ce49fc959ff38e206ac6ca 10240 science optional abyss_2.3.10-3_amd64.buildinfo b98769f1cb9658d509d1f36be115e83a 3400232 science optional abyss_2.3.10-3_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 18 Oct 2026 00:12:06 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: abyss Binary: abyss abyss-dbgsym Architecture: amd64 source Version: 2.3.10-3 Checksums-Md5: f9c3f1b308f17e2c91d8ab47158de01b 1313 abyss_2.3.10-3.dsc 02390d5e2ce67a15f50b4381a785d5f4 38706116 abyss-dbgsym_2.3.10-3_amd64.deb b98769f1cb9658d509d1f36be115e83a 3400232 abyss_2.3.10-3_amd64.deb Checksums-Sha1: 96b1162c3f5dac7aeb70fe27bb8c28b1d332504b 1313 abyss_2.3.10-3.dsc 0742e82ab8cba3850e8592a9660388f032eb5fdd 38706116 abyss-dbgsym_2.3.10-3_amd64.deb a8019613122d30ff01eaed8cb5800e084e7ca44d 3400232 abyss_2.3.10-3_amd64.deb Checksums-Sha256: c39341f83f9cfa848fe1a888c4bbb84633076ca4bd247ba6ec540033ed0be866 1313 abyss_2.3.10-3.dsc 314259a758c448f4f9d42e6b26ffef5d3e63153af8d4fbcd55160071b851d7ef 38706116 abyss-dbgsym_2.3.10-3_amd64.deb d5e112b30af0aa96b49a38757831bba117910c16234d67e4d014333a5bdb6816 3400232 abyss_2.3.10-3_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 18 Oct 2026 00:12:04 +0000 Build-Path: /build/abyss-Cm50Ye/abyss-2.3.10 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: architecture-properties (= 0.2.6+b2), autoconf (= 2.73-2), automake (= 1:1.19-2), autopoint (= 1.0-5), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-4), binutils (= 2.47-6), binutils-common (= 2.47-6), binutils-x86-64-linux-gnu (= 2.47-6), bsdextrautils (= 2.42.4-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), coreutils (= 9.10-1), cpp (= 4:16.1.0-3), cpp-15 (= 15.3.0-4), cpp-15-x86-64-linux-gnu (= 15.3.0-4), cpp-16 (= 16.2.0-3), cpp-16-x86-64-linux-gnu (= 16.2.0-3), cpp-x86-64-linux-gnu (= 4:16.1.0-3), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.5), debianutils (= 5.24), dh-autoreconf (= 23), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.11), dpkg-dev (= 1.23.11), dwz (= 0.17-1), file (= 1:5.47-4), findutils (= 4.11.0-3), fonts-font-awesome (= 7.3.0+dfsg-1), fonts-font-awesome-legacy (= 6-4), fonts-lato (= 2.015-1), g++ (= 4:16.1.0-3), g++-16 (= 16.2.0-3), g++-16-x86-64-linux-gnu (= 16.2.0-3), g++-x86-64-linux-gnu (= 4:16.1.0-3), gcc (= 4:16.1.0-3), gcc-15 (= 15.3.0-4), gcc-15-base (= 15.3.0-4), gcc-15-x86-64-linux-gnu (= 15.3.0-4), gcc-16 (= 16.2.0-3), gcc-16-base (= 16.2.0-3), gcc-16-x86-64-linux-gnu (= 16.2.0-3), gcc-x86-64-linux-gnu (= 4:16.1.0-3), gettext (= 1.0-5), gettext-base (= 1.0-5), gfortran-16 (= 16.2.0-3), gfortran-16-x86-64-linux-gnu (= 16.2.0-3), grep (= 3.12-1), groff-base (= 1.24.2-2), gzip (= 1.14-1), help2man (= 1.49.3), hostname (= 3.25), ibverbs-providers (= 65.0-1.1), init-system-helpers (= 1.69+nmu3), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.4.0-1), libamd-comgr3 (= 7.0.2+dfsg-3), libamdhip64-6 (= 6.4.3-5), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.2.0-3), libatomic1 (= 16.2.0-3), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.2.1-1), libaudit1 (= 1:4.2.1-1), libbinutils (= 2.47-6), libblkid1 (= 2.42.4-1), libboost-atomic1.92-dev (= 1.92.0-4), libboost-atomic1.92.0 (= 1.92.0-4), libboost-chrono1.92-dev (= 1.92.0-4), libboost-chrono1.92.0 (= 1.92.0-4), libboost-container1.92-dev (= 1.92.0-4), libboost-container1.92.0 (= 1.92.0-4), libboost-date-time1.92-dev (= 1.92.0-4), libboost-date-time1.92.0 (= 1.92.0-4), libboost-exception1.92-dev (= 1.92.0-4), libboost-graph-dev (= 1.92.0.1), libboost-graph1.92-dev (= 1.92.0-4), libboost-graph1.92.0 (= 1.92.0-4), libboost-math1.92-dev (= 1.92.0-4), libboost-math1.92.0 (= 1.92.0-4), libboost-random1.92-dev (= 1.92.0-4), libboost-random1.92.0 (= 1.92.0-4), libboost-regex1.92-dev (= 1.92.0-4), libboost-regex1.92.0 (= 1.92.0-4), libboost-serialization1.92-dev (= 1.92.0-4), libboost-serialization1.92.0 (= 1.92.0-4), libboost-test1.92-dev (= 1.92.0-4), libboost-test1.92.0 (= 1.92.0-4), libboost-thread1.92-dev (= 1.92.0-4), libboost-thread1.92.0 (= 1.92.0-4), libboost1.92-dev (= 1.92.0-4), libbrotli1 (= 1.2.0-4+b1), libbsd0 (= 0.12.2-3), libbtllib-dev (= 1.7.5+dfsg-2), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.43-7), libc-dev-bin (= 2.43-7), libc-gconv-modules-extra (= 2.43-7), libc6 (= 2.43-7), libc6-dev (= 2.43-7), libcap-ng0 (= 0.9.6-1), libcbor0.10 (= 0.10.2-2.2), libcc1-0 (= 16.2.0-3), libclang-common-21-dev (= 1:21.1.8-13), libcom-err2 (= 1.47.4-1+b2), libcpptoml-dev (= 0.1.1-3), libcrypt1 (= 1:4.5.2+20251210-1), libctf-nobfd0 (= 2.47-6), libctf0 (= 2.47-6), libcurl4-gnutls (= 8.23.0-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.5), libdeflate0 (= 1.25-1), libdpkg-perl (= 1.23.11), libdrm-amdgpu1 (= 2.4.134-3), libdrm-common (= 2.4.134-3), libdrm2 (= 2.4.134-3), libedit2 (= 3.1-20260512-1), libelf1t64 (= 0.196-1), libesmtp6 (= 1.1.0-3.2+b2), libevent-2.1-7t64 (= 2.1.13-stable-1), libevent-core-2.1-7t64 (= 2.1.13-stable-1), libevent-dev (= 2.1.13-stable-1), libevent-extra-2.1-7t64 (= 2.1.13-stable-1), libevent-openssl-2.1-7t64 (= 2.1.13-stable-1), libevent-pthreads-2.1-7t64 (= 2.1.13-stable-1), libexpat1 (= 2.9.0-1), libfabric1 (= 2.1.0-1.1+b2), libffi8 (= 3.8.0-2), libfido2-1 (= 1.17.0-2), libfile-stripnondeterminism-perl (= 1.15.1-1), libfuse3-4 (= 3.18.3-1), libgcc-15-dev (= 15.3.0-4), libgcc-16-dev (= 16.2.0-3), libgcc-s1 (= 16.2.0-3), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgfortran-16-dev (= 16.2.0-3), libgfortran5 (= 16.2.0-3), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgnutls30t64 (= 3.8.13-1), libgomp1 (= 16.2.0-3), libgprofng0 (= 2.47-6), libgssapi-krb5-2 (= 1.22.1-3), libhogweed6t64 (= 3.10.2-1+b1), libhsa-runtime64-1 (= 6.4.3+dfsg-5), libhtml-parser-perl (= 3.83-2+b3), libhtml-tagset-perl (= 3.24-1), libhts3t64 (= 1.24-3), libhtscodecs2 (= 1.6.7-1), libhwasan0 (= 16.2.0-3), libhwloc-dev (= 2.15.0-2), libhwloc-plugins (= 2.15.0-2), libhwloc15 (= 2.15.0-2), libibmad5 (= 65.0-1.1), libibumad3 (= 65.0-1.1), libibverbs-dev (= 65.0-1.1), libibverbs1 (= 65.0-1.1), libidn2-0 (= 2.3.8-5), libisl23 (= 0.28-1), libitm1 (= 16.2.0-3), libjansson4 (= 2.15.1-1), libjs-jquery (= 3.7.1+dfsg+~3.5.33-1), libjs-jquery-ui (= 1.14.2+dfsg-1), libk5crypto3 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libldap2 (= 2.6.14+dfsg-2+b1), libllvm21 (= 1:21.1.8-13), liblocale-gettext-perl (= 1.07-10+b2), liblsan0 (= 16.2.0-3), libltdl-dev (= 2.6.2-3), libltdl7 (= 2.6.2-3), liblzma5 (= 5.8.4-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.3.0-1), libmount1 (= 2.42.4-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libncurses6 (= 6.6+20260608-2), libncursesw6 (= 6.6+20260608-2), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.70.0-1), libnghttp3-9 (= 1.17.0-1), libngtcp2-16 (= 1.24.0-1), libngtcp2-crypto-gnutls8 (= 1.24.0-1), libnl-3-200 (= 3.12.0-2+b1), libnl-3-dev (= 3.12.0-2+b1), libnl-route-3-200 (= 3.12.0-2+b1), libnl-route-3-dev (= 3.12.0-2+b1), libnuma-dev (= 2.0.19-1+b2), libnuma1 (= 2.0.19-1+b2), libopenmpi-dev (= 6.0.0~rc2-2), libopenmpi40 (= 6.0.0~rc2-2), libp11-kit0 (= 0.26.5-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpciaccess0 (= 0.19-2), libpcre2-8-0 (= 10.48-3.1), libperl5.44 (= 5.44.0-1), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpmix2t64 (= 7.0.0~rc1-2), libprrte-bin (= 5.0.0~rc1-1), libprrte-dev (= 5.0.0~rc1-1), libprrte4 (= 5.0.0~rc1-1), libpsl5t64 (= 0.23.3-1), libpsm2-2 (= 11.2.185-2.1), libpython3-stdlib (= 3.14.7-3), libpython3.14-minimal (= 3.14.8-1), libpython3.14-stdlib (= 3.14.8-1), libquadmath0 (= 16.2.0-3), librdmacm1t64 (= 65.0-1.1), libreadline8t64 (= 8.3-4), libsasl2-2 (= 2.1.28+dfsg1-12), libsasl2-modules-db (= 2.1.28+dfsg1-12), libseccomp2 (= 2.6.1-1+b1), libselinux1 (= 3.11-2.1), libsframe3 (= 2.47-6), libsmartcols1 (= 2.42.4-1), libsparsehash-dev (= 2.0.4-2), libsqlite3-0 (= 3.53.4-2), libsqlite3-dev (= 3.53.4-2), libssh2-1t64 (= 1.11.1-6), libssl3t64 (= 3.6.5-1), libstdc++-16-dev (= 16.2.0-3), libstdc++6 (= 16.2.0-3), libsystemd-shared (= 262.1-1), libsystemd0 (= 262.1-1), libtasn1-6 (= 4.21.0-2+b1), libtext-markdown-perl (= 1.000031-5), libtext-multimarkdown-perl (= 1.000035-3), libtinfo6 (= 6.6+20260608-2), libtool (= 2.6.2-3), libtsan2 (= 16.2.0-3), libubsan1 (= 16.2.0-3), libucc1 (= 1.9.0-1), libuchardet0 (= 0.0.8-2+b2), libucx0 (= 1.22.0-2), libudev1 (= 262.1-1), libunistring5 (= 1.4.2-1), liburi-perl (= 5.37-1), libuuid1 (= 2.42.4-1), libx11-6 (= 2:1.8.13-1), libx11-data (= 2:1.8.13-1), libxau6 (= 1:1.0.11-1+b2), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2+b1), libxext6 (= 2:1.3.4-1+b4), libxml2-16 (= 2.15.4+dfsg-1), libxnvctrl0 (= 535.171.04-1+b3), libz3-4 (= 4.13.3-1.1), libze1 (= 1.32.0-1), libzstd1 (= 1.5.7+dfsg-4), linux-libc-dev (= 7.2.11-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-2), media-types (= 14.0.0), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), netbase (= 6.6), ocl-icd-libopencl1 (= 2.3.4-1+b1), openmpi-bin (= 6.0.0~rc2-2), openmpi-common (= 6.0.0~rc2-2), openssh-client (= 1:10.6p1-1), openssh-common (= 1:10.6p1-1), openssl-provider-legacy (= 3.6.5-1), patch (= 2.8-2), pci.ids (= 0.0~2026.09.23-1), perl (= 5.44.0-1), perl-base (= 5.44.0-1), perl-modules-5.44 (= 5.44.0-1), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), prrte-common (= 5.0.0~rc1-1), python3 (= 3.14.7-3), python3-minimal (= 3.14.7-3), python3.14 (= 3.14.8-1), python3.14-minimal (= 3.14.8-1), readline-common (= 8.3-4), samtools (= 1.24-2), sed (= 4.9-3), sensible-utils (= 0.0.26), systemd (= 262.1-1), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-6), tzdata (= 2026e-1), util-linux (= 2.42.4-1), wget (= 1.25.0-3), xz-utils (= 5.8.4-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1792251812" +------------------------------------------------------------------------------+ | Package contents Sun, 18 Oct 2026 00:12:06 +0000 | +------------------------------------------------------------------------------+ abyss-dbgsym_2.3.10-3_amd64.deb ------------------------------- new Debian package, version 2.0. size 38706116 bytes: control archive=2480 bytes. 2088 bytes, 12 lines control 4558 bytes, 43 lines md5sums Package: abyss-dbgsym Source: abyss Version: 2.3.10-3 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./usr/lib/debug/.build-id/e0/c11d8546630af8de6d299af9da2aa4e20137d1.debug drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/lib/debug/.build-id/ef/ -rw-r--r-- root/root 847504 2026-10-17 15:43 ./usr/lib/debug/.build-id/ef/74a33bee9731187f86b3b37343c34bd4df5a63.debug drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/lib/debug/.build-id/f0/ -rw-r--r-- root/root 1841352 2026-10-17 15:43 ./usr/lib/debug/.build-id/f0/cea3676214c48d09d9d3220670942327f35851.debug drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/share/ drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-10-17 15:43 ./usr/share/doc/abyss-dbgsym -> abyss abyss_2.3.10-3_amd64.deb ------------------------ new Debian package, version 2.0. size 3400232 bytes: control archive=2696 bytes. 761 bytes, 15 lines control 4847 bytes, 77 lines md5sums Package: abyss Version: 2.3.10-3 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 10343 Depends: make, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi40 (>= 6.0.0~rc2), 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. Commands: DistanceEst, abyss-fixmate, abyss-pe drwxr-xr-x root/root 0 2026-10-17 15:43 ./ drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/ drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/bin/ -rwxr-xr-x root/root 153880 2026-10-17 15:43 ./usr/bin/DistanceEst -rwxr-xr-x root/root 141568 2026-10-17 15:43 ./usr/bin/abyss-fixmate -rwxr-xr-x root/root 23209 2026-10-17 15:43 ./usr/bin/abyss-pe drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/lib/ drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/lib/abyss/ -rwxr-xr-x root/root 272680 2026-10-17 15:43 ./usr/lib/abyss/ABYSS -rwxr-xr-x root/root 330024 2026-10-17 15:43 ./usr/lib/abyss/ABYSS-P -rwxr-xr-x root/root 186640 2026-10-17 15:43 ./usr/lib/abyss/AdjList -rwxr-xr-x root/root 80136 2026-10-17 15:43 ./usr/lib/abyss/Consensus -rwxr-xr-x root/root 108824 2026-10-17 15:43 ./usr/lib/abyss/DAssembler -rwxr-xr-x root/root 153880 2026-10-17 15:43 ./usr/lib/abyss/DistanceEst -rwxr-xr-x root/root 157976 2026-10-17 15:43 ./usr/lib/abyss/DistanceEst-ssq -rwxr-xr-x root/root 186648 2026-10-17 15:43 ./usr/lib/abyss/KAligner -rwxr-xr-x root/root 235808 2026-10-17 15:43 ./usr/lib/abyss/MergeContigs -rwxr-xr-x root/root 203016 2026-10-17 15:43 ./usr/lib/abyss/MergePaths -rwxr-xr-x root/root 190744 2026-10-17 15:43 ./usr/lib/abyss/Overlap -rwxr-xr-x root/root 100600 2026-10-17 15:43 ./usr/lib/abyss/ParseAligns -rwxr-xr-x root/root 366872 2026-10-17 15:43 ./usr/lib/abyss/PathConsensus -rwxr-xr-x root/root 178424 2026-10-17 15:43 ./usr/lib/abyss/PathOverlap -rwxr-xr-x root/root 203032 2026-10-17 15:43 ./usr/lib/abyss/PopBubbles -rwxr-xr-x root/root 194840 2026-10-17 15:43 ./usr/lib/abyss/SimpleGraph -rwxr-xr-x root/root 194824 2026-10-17 15:43 ./usr/lib/abyss/abyss-align -rwxr-xr-x root/root 371072 2026-10-17 15:43 ./usr/lib/abyss/abyss-bloom -rwxr-xr-x root/root 395616 2026-10-17 15:43 ./usr/lib/abyss/abyss-bloom-dbg -rwxr-xr-x root/root 6491 2026-10-17 15:43 ./usr/lib/abyss/abyss-bloom-dist.mk -rwxr-xr-x root/root 1135 2026-10-17 15:43 ./usr/lib/abyss/abyss-bowtie -rwxr-xr-x root/root 1192 2026-10-17 15:43 ./usr/lib/abyss/abyss-bowtie2 -rwxr-xr-x root/root 1208 2026-10-17 15:43 ./usr/lib/abyss/abyss-bwa -rwxr-xr-x root/root 1454 2026-10-17 15:43 ./usr/lib/abyss/abyss-bwamem -rwxr-xr-x root/root 1362 2026-10-17 15:43 ./usr/lib/abyss/abyss-bwasw -rwxr-xr-x root/root 67832 2026-10-17 15:43 ./usr/lib/abyss/abyss-db-csv -rwxr-xr-x root/root 703 2026-10-17 15:43 ./usr/lib/abyss/abyss-db-txt -rwxr-xr-x root/root 2739 2026-10-17 15:43 ./usr/lib/abyss/abyss-dida -rwxr-xr-x root/root 88336 2026-10-17 15:43 ./usr/lib/abyss/abyss-fac -rwxr-xr-x root/root 2058 2026-10-17 15:43 ./usr/lib/abyss/abyss-fatoagp -rwxr-xr-x root/root 182552 2026-10-17 15:43 ./usr/lib/abyss/abyss-filtergraph -rwxr-xr-x root/root 141568 2026-10-17 15:43 ./usr/lib/abyss/abyss-fixmate -rwxr-xr-x root/root 141568 2026-10-17 15:43 ./usr/lib/abyss/abyss-fixmate-ssq -rwxr-xr-x root/root 108824 2026-10-17 15:43 ./usr/lib/abyss/abyss-gapfill -rwxr-xr-x root/root 88312 2026-10-17 15:43 ./usr/lib/abyss/abyss-gc -rwxr-xr-x root/root 100608 2026-10-17 15:43 ./usr/lib/abyss/abyss-index -rwxr-xr-x root/root 104704 2026-10-17 15:43 ./usr/lib/abyss/abyss-junction -rwxr-xr-x root/root 39 2026-10-17 15:43 ./usr/lib/abyss/abyss-kaligner -rwxr-xr-x root/root 141568 2026-10-17 15:43 ./usr/lib/abyss/abyss-layout -rwxr-xr-x root/root 108808 2026-10-17 15:43 ./usr/lib/abyss/abyss-longseqdist -rwxr-xr-x root/root 190736 2026-10-17 15:43 ./usr/lib/abyss/abyss-map -rwxr-xr-x root/root 194832 2026-10-17 15:43 ./usr/lib/abyss/abyss-map-ssq -rwxr-xr-x root/root 88352 2026-10-17 15:43 ./usr/lib/abyss/abyss-mergepairs -rwxr-xr-x root/root 211232 2026-10-17 15:43 ./usr/lib/abyss/abyss-overlap -rwxr-xr-x root/root 289072 2026-10-17 15:43 ./usr/lib/abyss/abyss-paired-dbg -rwxr-xr-x root/root 338216 2026-10-17 15:43 ./usr/lib/abyss/abyss-paired-dbg-mpi -rwxr-xr-x root/root 23209 2026-10-17 15:43 ./usr/lib/abyss/abyss-pe -rwxr-xr-x root/root 731544 2026-10-17 15:43 ./usr/lib/abyss/abyss-rresolver-short -rwxr-xr-x root/root 4501 2026-10-17 15:43 ./usr/lib/abyss/abyss-samtoafg -rwxr-xr-x root/root 256272 2026-10-17 15:43 ./usr/lib/abyss/abyss-scaffold -rwxr-xr-x root/root 235888 2026-10-17 15:43 ./usr/lib/abyss/abyss-sealer -rwxr-xr-x root/root 671 2026-10-17 15:43 ./usr/lib/abyss/abyss-stack-size -rwxr-xr-x root/root 209 2026-10-17 15:43 ./usr/lib/abyss/abyss-tabtomd -rwxr-xr-x root/root 162048 2026-10-17 15:43 ./usr/lib/abyss/abyss-todot -rwxr-xr-x root/root 71952 2026-10-17 15:43 ./usr/lib/abyss/abyss-tofastq -rwxr-xr-x root/root 272784 2026-10-17 15:43 ./usr/lib/abyss/konnector -rwxr-xr-x root/root 80152 2026-10-17 15:43 ./usr/lib/abyss/logcounter drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/share/ drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/share/doc-base/ -rw-r--r-- root/root 226 2026-10-17 15:43 ./usr/share/doc-base/abyss.abyss-flowcharts drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/share/doc/abyss/ -rw-r--r-- root/root 556 2026-10-17 15:43 ./usr/share/doc/abyss/CITATION.bib -rw-r--r-- root/root 1861 2026-10-17 15:43 ./usr/share/doc/abyss/CITATION.md -rw-r--r-- root/root 32190 2026-10-17 15:43 ./usr/share/doc/abyss/README.html -rw-r--r-- root/root 9525 2026-10-17 15:43 ./usr/share/doc/abyss/README.md.gz -rw-r--r-- root/root 182 2026-10-17 15:43 ./usr/share/doc/abyss/README.test -rw-r--r-- root/root 1130 2026-10-17 15:43 ./usr/share/doc/abyss/changelog.Debian.gz -rw-r--r-- root/root 16508 2024-10-18 20:51 ./usr/share/doc/abyss/changelog.gz -rw-r--r-- root/root 6859 2026-10-17 15:43 ./usr/share/doc/abyss/copyright -rw-r--r-- root/root 66778 2026-10-17 15:43 ./usr/share/doc/abyss/flowchart.pdf.gz -rw-r--r-- root/root 22664 2026-10-17 15:43 ./usr/share/doc/abyss/flowchart_simplified.pdf.gz -rw-r--r-- root/root 677 2026-10-17 15:43 ./usr/share/doc/abyss/run-unit-test drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/share/doc/abyss/test-data/ -rw-r--r-- root/root 743013 2026-10-17 15:43 ./usr/share/doc/abyss/test-data/reads1.fastq.gz -rw-r--r-- root/root 743377 2026-10-17 15:43 ./usr/share/doc/abyss/test-data/reads2.fastq.gz drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/share/man/ drwxr-xr-x root/root 0 2026-10-17 15:43 ./usr/share/man/man1/ -rw-r--r-- root/root 1021 2026-10-17 15:43 ./usr/share/man/man1/DistanceEst.1.gz -rw-r--r-- root/root 791 2026-10-17 15:43 ./usr/share/man/man1/abyss-fixmate.1.gz -rw-r--r-- root/root 3562 2026-10-17 15:43 ./usr/share/man/man1/abyss-pe.1.gz +------------------------------------------------------------------------------+ | Post Build Sun, 18 Oct 2026 00:12:07 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 18 Oct 2026 00:12:07 +0000 | +------------------------------------------------------------------------------+ Purging /build/abyss-Cm50Ye Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 18 Oct 2026 00:12:09 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 787924 Build-Time: 465 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 24 Job: /srv/debomatic/incoming/abyss_2.3.10-3.dsc Machine Architecture: amd64 Package: abyss Package-Time: 493 Source-Version: 2.3.10-3 Space: 787924 Status: successful Version: 2.3.10-3 -------------------------------------------------------------------------------- Finished at 2026-10-18T00:12:05Z Build needed 00:08:13, 787924k disk space