https://launchpad.net/ubuntu/+source/abyss/2.3.5+dfsg-1/+build/23747339 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-079 5.4.0-110-generic #124-Ubuntu SMP Thu Apr 14 19:46:19 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_212~550~ubuntu20.04.1 python3-lpbuildd_212~550~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.4 dpkg-dev_1.19.7ubuntu3 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 14 May 23:16:28 ntpdate[1930]: adjust time server 10.131.248.1 offset 0.000884 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23747339 --image-type chroot /home/buildd/filecache-default/4bae5e21afd462667e3742a3b80ddb4ff02f2b5f Creating target for build PACKAGEBUILD-23747339 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23747339 Starting target for build PACKAGEBUILD-23747339 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23747339 'deb http://ftpmaster.internal/ubuntu kinetic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu kinetic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu kinetic-updates main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu kinetic-proposed main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-23747339 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23747339 Updating target for build PACKAGEBUILD-23747339 Get:1 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 Packages [1398 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/restricted amd64 Packages [129 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/restricted Translation-en [18.6 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/universe amd64 Packages [14.2 MB] Get:10 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5694 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/multiverse amd64 Packages [217 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/multiverse Translation-en [112 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 Packages [160 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic-proposed/main Translation-en [58.4 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic-proposed/restricted amd64 Packages [39.6 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/restricted Translation-en [6720 B] Get:17 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 Packages [804 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic-proposed/universe Translation-en [285 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic-proposed/multiverse amd64 Packages [4844 B] Get:20 http://ftpmaster.internal/ubuntu kinetic-proposed/multiverse Translation-en [6528 B] Fetched 24.2 MB in 2s (10.4 MB/s) Reading package lists... W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (restricted/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (universe/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (multiverse/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (restricted/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (universe/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (multiverse/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: util-linux-extra The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu bsdutils cpp-11 dash debianutils dpkg dpkg-dev g++-11 gcc-11 gcc-11-base gcc-12-base libasan6 libassuan0 libatomic1 libbinutils libblkid1 libcc1-0 libctf-nobfd0 libctf0 libdpkg-perl libgcc-11-dev libgcc-s1 libgnutls30 libgomp1 libgpg-error0 libip4tc2 libitm1 libjson-c5 liblsan0 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpng16-16 libquadmath0 libreadline8 libseccomp2 libsmartcols1 libsqlite3-0 libssl3 libstdc++-11-dev libstdc++6 libtinfo6 libtsan0 libubsan1 libuuid1 libzstd1 linux-libc-dev lto-disabled-list mount ncurses-base ncurses-bin openssl pinentry-curses readline-common util-linux 64 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 70.3 MB of archives. After this operation, 757 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 bsdutils amd64 1:2.38-4ubuntu1 [80.7 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic/main amd64 debianutils amd64 5.7-0.2 [103 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [270 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 dpkg amd64 1.21.7ubuntu3 [1342 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-8 [88.0 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 ncurses-bin amd64 6.3+20220423-2 [183 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libblkid1 amd64 2.38-4ubuntu1 [103 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libmount1 amd64 2.38-4ubuntu1 [121 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libsmartcols1 amd64 2.38-4ubuntu1 [50.8 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 util-linux-extra amd64 2.38-4ubuntu1 [83.8 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 util-linux amd64 2.38-4ubuntu1 [1069 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpam0g amd64 1.4.0-13ubuntu1 [60.2 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpam-modules-bin amd64 1.4.0-13ubuntu1 [37.6 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpam-modules amd64 1.4.0-13ubuntu1 [278 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 mount amd64 2.38-4ubuntu1 [114 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libatomic1 amd64 12.1.0-2ubuntu1 [10.4 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libubsan1 amd64 12.1.0-2ubuntu1 [969 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 gcc-12-base amd64 12.1.0-2ubuntu1 [18.8 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libstdc++6 amd64 12.1.0-2ubuntu1 [679 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libquadmath0 amd64 12.1.0-2ubuntu1 [152 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 liblsan0 amd64 12.1.0-2ubuntu1 [1060 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libitm1 amd64 12.1.0-2ubuntu1 [29.5 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libgomp1 amd64 12.1.0-2ubuntu1 [125 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libcc1-0 amd64 12.1.0-2ubuntu1 [46.6 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libgcc-s1 amd64 12.1.0-2ubuntu1 [54.2 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libgpg-error0 amd64 1.45-2 [69.0 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpam-runtime all 1.4.0-13ubuntu1 [40.2 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpcre2-8-0 amd64 10.40-1 [227 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpcre3 amd64 2:8.39-14 [245 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libncursesw6 amd64 6.3+20220423-2 [146 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libncurses6 amd64 6.3+20220423-2 [110 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libtinfo6 amd64 6.3+20220423-2 [99.6 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libuuid1 amd64 2.38-4ubuntu1 [23.2 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 libp11-kit0 amd64 0.24.1-1 [257 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgnutls30 amd64 3.7.4-2ubuntu1 [972 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main amd64 libseccomp2 amd64 2.5.4-1ubuntu1 [46.3 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libip4tc2 amd64 1.8.7-1ubuntu6 [19.7 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjson-c5 amd64 0.16-1 [33.7 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 readline-common all 8.1.2-1.2 [53.6 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libreadline8 amd64 8.1.2-1.2 [153 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libsqlite3-0 amd64 3.38.5-1 [646 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libssl3 amd64 3.0.3-0ubuntu1 [1884 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 openssl amd64 3.0.3-0ubuntu1 [1173 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libpng16-16 amd64 1.6.37-5 [187 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libctf-nobfd0 amd64 2.38-4ubuntu1 [105 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libctf0 amd64 2.38-4ubuntu1 [101 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.38-4ubuntu1 [2304 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libbinutils amd64 2.38-4ubuntu1 [651 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 binutils amd64 2.38-4ubuntu1 [3190 B] Get:51 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 binutils-common amd64 2.38-4ubuntu1 [221 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 g++-11 amd64 11.3.0-1ubuntu1 [11.4 MB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++-11-dev amd64 11.3.0-1ubuntu1 [2087 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 libasan6 amd64 11.3.0-1ubuntu1 [2284 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-11 amd64 11.3.0-1ubuntu1 [20.1 MB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-11-dev amd64 11.3.0-1ubuntu1 [2516 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtsan0 amd64 11.3.0-1ubuntu1 [2261 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main amd64 cpp-11 amd64 11.3.0-1ubuntu1 [9968 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-11-base amd64 11.3.0-1ubuntu1 [21.1 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 dpkg-dev all 1.21.7ubuntu3 [1070 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libdpkg-perl all 1.21.7ubuntu3 [236 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main amd64 lto-disabled-list all 25 [12.6 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic/main amd64 libassuan0 amd64 2.5.5-3 [37.4 kB] Get:64 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 linux-libc-dev amd64 5.15.0-28.29 [1345 kB] Get:65 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 pinentry-curses amd64 1.2.0-1 [35.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 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Setting up binutils-x86-64-linux-gnu (2.38-4ubuntu1) ... Setting up binutils (2.38-4ubuntu1) ... Setting up dpkg-dev (1.21.7ubuntu3) ... Setting up libstdc++-11-dev:amd64 (11.3.0-1ubuntu1) ... Setting up gcc-11 (11.3.0-1ubuntu1) ... Setting up g++-11 (11.3.0-1ubuntu1) ... Processing triggers for debianutils (5.7-0.2) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23747339 amd64 kinetic-proposed -c chroot:build-PACKAGEBUILD-23747339 --arch=amd64 --dist=kinetic-proposed --nolog -A abyss_2.3.5+dfsg-1.dsc Initiating build PACKAGEBUILD-23747339 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-110-generic #124-Ubuntu SMP Thu Apr 14 19:46:19 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-079.buildd +==============================================================================+ | abyss 2.3.5+dfsg-1 (amd64) Sat, 14 May 2022 23:16:46 +0000 | +==============================================================================+ Package: abyss Version: 2.3.5+dfsg-1 Source Version: 2.3.5+dfsg-1 Distribution: kinetic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23747339/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/abyss-A6AVZD/resolver-liKigW' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- abyss_2.3.5+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/abyss-A6AVZD/abyss-2.3.5+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/abyss-A6AVZD' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man, debhelper, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man, debhelper, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [449 B] Get:5 copy:/<>/apt_archive ./ Packages [519 B] Fetched 1925 B in 0s (172 kB/s) Reading package lists... Reading package lists... W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (restricted/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (restricted/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (multiverse/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (multiverse/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran-11 groff-base help2man ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libboost-graph-dev libboost-graph1.74-dev libboost-graph1.74.0 libboost-regex1.74-dev libboost-regex1.74.0 libboost-serialization1.74-dev libboost-serialization1.74.0 libboost-test1.74-dev libboost-test1.74.0 libboost1.74-dev libbrotli1 libbsd0 libcbor0.8 libcurl3-gnutls libdebhelper-perl libdw1 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-11-dev libgfortran5 libglib2.0-0 libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu71 libjs-jquery libjs-jquery-ui libldap-2.5-0 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsparsehash-dev libsqlite3-dev libssh-4 libsub-override-perl libtext-markdown-perl libtext-multimarkdown-perl libtool libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-11-multilib gfortran-11-doc libcoarrays-dev groff graphviz libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libdata-dump-perl libhwloc-contrib-plugins icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils sqlite3-doc gcj-jdk libbusiness-isbn-perl libwww-perl m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libhttp-message-perl javascript-common libldap-common libcoarrays-openmpi-dev publicsuffix libsasl2-modules xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran-11 groff-base help2man ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libboost-graph-dev libboost-graph1.74-dev libboost-graph1.74.0 libboost-regex1.74-dev libboost-regex1.74.0 libboost-serialization1.74-dev libboost-serialization1.74.0 libboost-test1.74-dev libboost-test1.74.0 libboost1.74-dev libbrotli1 libbsd0 libcbor0.8 libcurl3-gnutls libdebhelper-perl libdw1 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-11-dev libgfortran5 libglib2.0-0 libhtml-parser-perl libhtml-tagset-perl libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu71 libjs-jquery libjs-jquery-ui libldap-2.5-0 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsparsehash-dev libsqlite3-dev libssh-4 libsub-override-perl libtext-markdown-perl libtext-multimarkdown-perl libtool libuchardet0 libucx0 liburi-perl libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 117 newly installed, 0 to remove and 0 not upgraded. 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[22.5 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpipeline1 amd64 1.5.6-1 [23.1 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpsl5 amd64 0.21.0-1.2build2 [58.4 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxau6 amd64 1:1.0.9-1build5 [7634 B] Get:24 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu5 [10.9 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxcb1 amd64 1.14-3ubuntu3 [49.0 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main amd64 libx11-data all 2:1.7.5-1 [119 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main amd64 libx11-6 amd64 2:1.7.5-1 [666 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxext6 amd64 2:1.3.4-1build1 [31.8 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main amd64 man-db amd64 2.10.2-1 [1187 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main amd64 openssh-client amd64 1:9.0p1-1 [897 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsigsegv2 amd64 2.13-1ubuntu3 [14.6 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main amd64 m4 amd64 1.4.18-5ubuntu2 [199 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 autoconf all 2.71-2 [338 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 autopoint all 0.21-4ubuntu4 [422 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libdebhelper-perl all 13.7.1ubuntu1 [66.9 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libtool all 2.4.7-4 [166 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main amd64 dh-autoreconf all 20 [16.1 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:42 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:44 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libdw1 amd64 0.187-1 [247 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main amd64 debugedit amd64 1:5.0-4build1 [47.2 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 dwz amd64 0.14-1build2 [105 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 gettext amd64 0.21-4ubuntu4 [868 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 debhelper all 13.7.1ubuntu1 [940 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libgfortran5 amd64 12.1.0-2ubuntu1 [875 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgfortran-11-dev amd64 11.3.0-1ubuntu1 [842 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 gfortran-11 amd64 11.3.0-1ubuntu1 [11.2 MB] Get:54 http://ftpmaster.internal/ubuntu kinetic/universe amd64 help2man amd64 1.49.2 [197 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnl-3-200 amd64 3.5.0-0.1 [59.1 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnl-route-3-200 amd64 3.5.0-0.1 [180 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 libibverbs1 amd64 39.0-1 [69.3 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main amd64 ibverbs-providers amd64 39.0-1 [341 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 icu-devtools amd64 71.1-3 [201 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libboost1.74-dev amd64 1.74.0-14ubuntu4 [9616 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libboost-regex1.74.0 amd64 1.74.0-14ubuntu4 [511 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 libboost-graph1.74.0 amd64 1.74.0-14ubuntu4 [304 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libicu-dev amd64 71.1-3 [11.6 MB] Get:64 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libboost-regex1.74-dev amd64 1.74.0-14ubuntu4 [596 kB] Get:65 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libboost-serialization1.74.0 amd64 1.74.0-14ubuntu4 [327 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libboost-serialization1.74-dev amd64 1.74.0-14ubuntu4 [375 kB] Get:67 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 libboost-test1.74.0 amd64 1.74.0-14ubuntu4 [445 kB] Get:68 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 libboost-test1.74-dev amd64 1.74.0-14ubuntu4 [564 kB] Get:69 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 libboost-graph1.74-dev amd64 1.74.0-14ubuntu4 [335 kB] Get:70 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libboost-graph-dev amd64 1.74.0.3ubuntu7 [3348 B] Get:71 http://ftpmaster.internal/ubuntu kinetic/main amd64 libbrotli1 amd64 1.0.9-2build6 [315 kB] Get:72 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg2-3ubuntu1 [20.8 kB] Get:73 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsasl2-2 amd64 2.1.27+dfsg2-3ubuntu1 [53.9 kB] Get:74 http://ftpmaster.internal/ubuntu kinetic/main amd64 libldap-2.5-0 amd64 2.5.11+dfsg-1~exp1ubuntu3 [184 kB] Get:75 http://ftpmaster.internal/ubuntu kinetic/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:76 http://ftpmaster.internal/ubuntu kinetic/main amd64 libssh-4 amd64 0.9.6-2build1 [184 kB] Get:77 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libcurl3-gnutls amd64 7.83.1-1 [281 kB] Get:78 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libevent-2.1-7 amd64 2.1.12-stable-5 [148 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-5 [94.5 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-5 [65.5 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-5 [7754 B] Get:82 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-5 [15.8 kB] Get:83 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libevent-dev amd64 2.1.12-stable-5 [278 kB] Get:84 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.1 [170 kB] Get:85 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libpsm2-2 amd64 11.2.185-1 [182 kB] Get:86 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Get:96 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnl-3-dev amd64 3.5.0-0.1 [101 kB] Get:97 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnl-route-3-dev amd64 3.5.0-0.1 [202 kB] Get:98 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpciaccess0 amd64 0.16-3 [19.1 kB] Get:99 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu1 [11.5 kB] Get:100 http://ftpmaster.internal/ubuntu kinetic/universe amd64 ocl-icd-libopencl1 amd64 2.2.14-3 [39.1 kB] Get:101 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 libhwloc-plugins amd64 2.7.1-1 [15.6 kB] Get:102 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libpmix2 amd64 4.1.2-2ubuntu1 [604 kB] Get:103 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libucx0 amd64 1.12.1-1 [879 kB] Get:104 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libopenmpi3 amd64 4.1.3-2ubuntu1 [2407 kB] Get:105 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnuma-dev amd64 2.0.14-3ubuntu2 [35.9 kB] Get:106 http://ftpmaster.internal/ubuntu kinetic-proposed/universe amd64 libhwloc-dev amd64 2.7.1-1 [252 kB] Get:107 http://ftpmaster.internal/ubuntu kinetic/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu9 [164 kB] Get:108 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libpmix-dev amd64 4.1.2-2ubuntu1 [805 kB] Get:109 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libsparsehash-dev all 2.0.3-2 [71.7 kB] Get:110 http://ftpmaster.internal/ubuntu kinetic-proposed/main amd64 libsqlite3-dev amd64 3.38.5-1 [848 kB] Get:111 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libtext-markdown-perl all 1.000031-3 [29.0 kB] Get:112 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libtext-multimarkdown-perl all 1.000035-2 [23.9 kB] Get:113 http://ftpmaster.internal/ubuntu kinetic/universe amd64 openmpi-common all 4.1.3-2ubuntu1 [163 kB] Get:114 http://ftpmaster.internal/ubuntu kinetic/universe amd64 openmpi-bin amd64 4.1.3-2ubuntu1 [116 kB] Get:115 http://ftpmaster.internal/ubuntu kinetic/main amd64 pkg-config amd64 0.29.2-1ubuntu3 [48.2 kB] Get:116 http://ftpmaster.internal/ubuntu kinetic/main amd64 libibverbs-dev amd64 39.0-1 [628 kB] Get:117 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libopenmpi-dev amd64 4.1.3-2ubuntu1 [867 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 73.0 MB in 1s (112 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 13506 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-4build3_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4build3) ... Selecting previously unselected package libmd0:amd64. Preparing to unpack .../001-libmd0_1.0.4-1build1_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-1build1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../002-libbsd0_0.11.6-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.6-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../003-libelf1_0.187-1_amd64.deb ... Unpacking libelf1:amd64 (0.187-1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../004-libglib2.0-0_2.72.1-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.72.1-1) ... Selecting previously unselected package libicu71:amd64. Preparing to unpack .../005-libicu71_71.1-3_amd64.deb ... Unpacking libicu71:amd64 (71.1-3) ... 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Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnuma-dev:amd64 (2.0.14-3ubuntu2) ... Setting up libnl-route-3-200:amd64 (3.5.0-0.1) ... Setting up help2man (1.49.2) ... Setting up libjs-jquery-ui (1.13.1+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-5) ... Setting up gfortran-11 (11.3.0-1ubuntu1) ... Setting up autoconf (2.71-2) ... Setting up libboost-serialization1.74-dev:amd64 (1.74.0-14ubuntu4) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up libboost-regex1.74-dev:amd64 (1.74.0-14ubuntu4) ... Setting up libnl-3-dev:amd64 (3.5.0-0.1) ... Setting up groff-base (1.22.4-8build1) ... Setting up libhtml-parser-perl:amd64 (3.78-1) ... Setting up debugedit (1:5.0-4build1) ... Setting up libx11-6:amd64 (2:1.7.5-1) ... Setting up libtext-multimarkdown-perl (1.000035-2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libibverbs1:amd64 (39.0-1) ... Setting up ibverbs-providers:amd64 (39.0-1) ... Setting up openssh-client (1:9.0p1-1) ... update-alternatives: using /usr/bin/ssh to provide /usr/bin/rsh (rsh) in auto mode update-alternatives: using /usr/bin/slogin to provide /usr/bin/rlogin (rlogin) in auto mode update-alternatives: using /usr/bin/scp to provide /usr/bin/rcp (rcp) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1build1) ... Setting up libcurl3-gnutls:amd64 (7.83.1-1) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu1) ... Setting up dh-autoreconf (20) ... 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Setting up openmpi-bin (4.1.3-2ubuntu1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.3-2ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any-amd64 arm64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-110-generic #124-Ubuntu SMP Thu Apr 14 19:46:19 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.38-4ubuntu1 dpkg-dev_1.21.7ubuntu3 g++-11_11.3.0-1ubuntu1 gcc-11_11.3.0-1ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-1ubuntu1 libstdc++6_12.1.0-2ubuntu1 linux-libc-dev_5.15.0-28.29 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu2 apt_2.4.5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-4ubuntu4 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libuchardet0_0.0.7-1build2 libucx0_1.12.1-1 libudev1_249.11-0ubuntu3.1 libunistring2_1.0-1 liburi-perl_5.10-1 libuuid1_2.38-4ubuntu1 libx11-6_2:1.7.5-1 libx11-data_2:1.7.5-1 libxau6_1:1.0.9-1build5 libxcb1_1.14-3ubuntu3 libxdmcp6_1:1.1.3-0ubuntu5 libxext6_2:1.3.4-1build1 libxml2_2.9.14+dfsg-1 libxnvctrl0_510.47.03-0ubuntu1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.15.0-28.29 lockfile-progs_0.1.19build1 login_1:4.8.1-2ubuntu2 logsave_1.46.5-2ubuntu1 lsb-base_11.1.0ubuntu4 lto-disabled-list_25 m4_1.4.18-5ubuntu2 make_4.3-4.1build1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 mount_2.38-4ubuntu1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 ocl-icd-libopencl1_2.2.14-3 openmpi-bin_4.1.3-2ubuntu1 openmpi-common_4.1.3-2ubuntu1 openssh-client_1:9.0p1-1 openssl_3.0.3-0ubuntu1 optipng_0.7.7-2build1 passwd_1:4.8.1-2ubuntu2 patch_2.7.6-7build2 perl_5.34.0-3ubuntu1 perl-base_5.34.0-3ubuntu1 perl-modules-5.34_5.34.0-3ubuntu1 pinentry-curses_1.2.0-1 pkg-config_0.29.2-1ubuntu3 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-6ubuntu2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 systemd_249.11-0ubuntu3.1 systemd-sysv_249.11-0ubuntu3.1 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build3 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.5-2ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu9 zlib1g-dev_1:1.2.11.dfsg-2ubuntu9 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: abyss Binary: abyss Architecture: any-amd64 arm64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha Version: 2.3.5+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe Homepage: https://github.com/bcgsc/abyss Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/abyss Vcs-Git: https://salsa.debian.org/med-team/abyss.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl , libsqlite3-dev, pkg-config, help2man, debhelper Package-List: abyss deb science optional arch=any-amd64,arm64,mips64el,ppc64el,s390x,ia64,ppc64,riscv64,sparc64,alpha Checksums-Sha1: 96d180cd0c80c0e770d1cdfc20f33de7ac733850 1514856 abyss_2.3.5+dfsg.orig.tar.xz 592327fb612854734d8f925e861efb0b94957ab6 1497572 abyss_2.3.5+dfsg-1.debian.tar.xz Checksums-Sha256: 6bf37999b640b8d366824f40f9842cd9bb4607d545a2350da4c80fcb84b4969e 1514856 abyss_2.3.5+dfsg.orig.tar.xz 65eac7b2c3a2f9052ad687096139ff2c167152ba5a021abcc8d986438f01fb44 1497572 abyss_2.3.5+dfsg-1.debian.tar.xz Files: 9efce3721a5f50b31db2827444f6d381 1514856 abyss_2.3.5+dfsg.orig.tar.xz 59c5e02162482b6cb9bbf55d681d7a79 1497572 abyss_2.3.5+dfsg-1.debian.tar.xz Dgit: 8f945677716d9ecab73fa6f4d9fdfded4fb686b1 debian archive/debian/2.3.5+dfsg-1 https://git.dgit.debian.org/abyss -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmJ/o5oUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdr6rQ//SAzW8nuHH4+HB5FyvJZITwiff12e Hub9o/L7SulwsLh1q9Rearb/bBQZfxboE7WP37ycW1ti/8EGP+NtqDa1XYJJAaJw 4AypFgfMI7a/XFrLVxeZcbqmlZfRPxn1VZeevuSfOsH7oet20jYkw1f4nQi9jQrb 3U5e+VS1MjmJp6kqhO/iBVHXoQHgxghOVAubjJx6Rap0hHAD3fhIvI+orkqqGc4a GxQj/AtF7V/AQlyHNyZOQ0a5qp4qKRWhcBfl+F18R7K8/DMxgttp8zesIfc/PJsx 06Fen6sapBP7ZEJwdQ69X3g+FStGs5lZG2cr3Ya7NCd+pXLbNqpMFZK1X+3cGdLS 2Ff4U20Npz2kBqyQIG997mbbGcqEQLq/Bvsfz29v0udwX46YFNhpB5V68c3qSzCG gP8ETdHTz4dD3TP9AS36TelcYyfMexYgNMTdSEGu/unjE7LWX/niShy1UHtKp9Jd I46GeywTP16BgXzbYZ5sLP0+1UnujMzKdT9SROJDfMHpWWLA81xxvHdVTdFNaoPE NRV+dF/JedbLygJfKegGnVPrECb58PKXRMJ3YTX0haklcu8+lNqYH7xk0m0ImCuJ M1cWpnjAx8Mi1cTWWNPcDcT7mBFIgTUqtiz4lzGZZcbN0wA6fTekXrYVS6JAyHp1 KEw2XijC6UXCrXc= =YUgk -----END PGP SIGNATURE----- gpgv: Signature made Sat May 14 12:42:02 2022 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./abyss_2.3.5+dfsg-1.dsc dpkg-source: info: extracting abyss in /<> dpkg-source: info: unpacking abyss_2.3.5+dfsg.orig.tar.xz dpkg-source: info: unpacking abyss_2.3.5+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying fix-privacy-breach.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-23747339 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23747339 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23747339 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.3.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:25: installing './ar-lib' configure.ac:16: installing './compile' configure.ac:80: installing './config.guess' configure.ac:80: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether g++ supports C++11 features with -std=c++11... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether 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 whether UID '2001' is supported by ustar format... yes checking whether GID '2501' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking dependency style of g++ -std=c++11... none checking for gawk... (cached) mawk checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=c++11 accepts -g... (cached) yes checking for g++ -std=c++11 option to enable C++11 features... (cached) none needed checking for ranlib... ranlib checking for ghc... no ./configure: line 7029: : command not found 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... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for std::hash... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... yes checking for dup2... yes checking for gethostname... yes checking for getopt_long... yes checking for getpagesize... yes checking for memset... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking for fork... yes checking for vfork... yes checking for vprintf... yes checking for working fork... yes checking for working vfork... (cached) yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for GNU libc compatible realloc... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether HOST_NAME_MAX is declared... yes checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking for functional... yes checking for tr1/functional... yes checking for boost/functional/hash.hpp... yes checking for boost/property_map/property_map.hpp... yes checking for google/sparse_hash_map... yes checking for unordered_map... yes checking for tr1/unordered_map... yes checking for unordered_set... yes checking for tr1/unordered_set... yes checking for boost/unordered_set.hpp... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for g++ -std=c++11 option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating vendor/gtest-1.7.0/Makefile config.status: creating RResolver/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating vendor/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build make -j4 make[2]: Entering directory '/<>' make all-recursive make[3]: Entering directory '/<>' Making all in bin make[4]: Entering directory '/<>/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/bin' Making all in doc make[4]: Entering directory '/<>/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/doc' Making all in Common make[4]: Entering directory '/<>/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc rm -f libcommon.a ar cru 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 ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcommon.a make[4]: Leaving directory '/<>/Common' Making all in Graph make[4]: Entering directory '/<>/Graph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L. -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Graph' Making all in DataLayer make[4]: Entering directory '/<>/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc rm -f libdatalayer.a ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/DataLayer' Making all in DataBase make[4]: Entering directory '/<>/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 cru libdb.a libdb_a-DB.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a make[4]: Leaving directory '/<>/DataBase' Making all in FMIndex make[4]: Entering directory '/<>/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc rm -f libfmindex.a ar cru libfmindex.a libfmindex_a-bit_array.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfmindex.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/FMIndex' Making all in Assembly make[4]: Entering directory '/<>/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc rm -f libassembly.a ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libassembly.a make[4]: Leaving directory '/<>/Assembly' Making all in dialign make[4]: Entering directory '/<>/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.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, | ^~~~~~~~~~~ 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, | ^~~~~~~~~~~ diag.c:1456:17: warning: ‘real_calc_weight’ is static but used in inline function ‘find_diags_dyn’ which is not static 1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); | ^~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c io.c: In function ‘read_scr_matrix’: io.c:270:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 270 | fscanf( fp, "%i", &is); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:282:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 282 | fscanf(fp, "%s\n", rline); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘read_diag_prob_dist’: io.c:371:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdialign.a gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm make[4]: Leaving directory '/<>/dialign' Making all in Align make[4]: Entering directory '/<>/Align' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc rm -f libalign.a ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libalign.a g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/Align' Making all in ABYSS make[4]: Entering directory '/<>/ABYSS' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/ABYSS' Making all in Parallel make[4]: Entering directory '/<>/Parallel' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm make[4]: Leaving directory '/<>/Parallel' Making all in Bloom make[4]: Entering directory '/<>/Bloom' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/Bloom' Making all in BloomDBG make[4]: Entering directory '/<>/BloomDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/BloomDBG' Making all in Konnector make[4]: Entering directory '/<>/Konnector' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/Konnector' Making all in Consensus make[4]: Entering directory '/<>/Consensus' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Consensus' Making all in DAssembler make[4]: Entering directory '/<>/DAssembler' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/DAssembler' Making all in DistanceEst make[4]: Entering directory '/<>/DistanceEst' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/DistanceEst' Making all in KAligner make[4]: Entering directory '/<>/KAligner' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/KAligner' Making all in Layout make[4]: Entering directory '/<>/Layout' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Layout' Making all in LogKmerCount make[4]: Entering directory '/<>/LogKmerCount' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/LogKmerCount' Making all in Map make[4]: Entering directory '/<>/Map' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/Map' Making all in MergePaths make[4]: Entering directory '/<>/MergePaths' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 make[4]: Leaving directory '/<>/MergePaths' Making all in Overlap make[4]: Entering directory '/<>/Overlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/Overlap' Making all in PairedDBG make[4]: Entering directory '/<>/PairedDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KmerPair.o KmerPair.cc rm -f libpaireddbg.a ar cru libpaireddbg.a KmerPair.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpaireddbg.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/<>/ParseAligns' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/<>/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/<>/PathOverlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/<>/PopBubbles' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/PopBubbles' Making all in Scaffold make[4]: Entering directory '/<>/Scaffold' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/<>/SimpleGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/<>/kmerprint' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/kmerprint' Making all in FilterGraph make[4]: Entering directory '/<>/FilterGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/FilterGraph' Making all in GapFiller make[4]: Entering directory '/<>/GapFiller' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/GapFiller' Making all in Sealer make[4]: Entering directory '/<>/Sealer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/Sealer' Making all in RResolver make[4]: Entering directory '/<>/RResolver' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_rresolver_short-RResolverShort.o `test -f 'RResolverShort.cpp' || echo './'`RResolverShort.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-RAlgorithmsShort.o `test -f 'RAlgorithmsShort.cpp' || echo './'`RAlgorithmsShort.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-BloomFilters.o `test -f 'BloomFilters.cpp' || echo './'`BloomFilters.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-SequenceTree.o `test -f 'SequenceTree.cpp' || echo './'`SequenceTree.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-RUtils.o `test -f 'RUtils.cpp' || echo './'`RUtils.cpp rm -f libralgorithmsshort.a ar cru libralgorithmsshort.a libralgorithmsshort_a-RAlgorithmsShort.o libralgorithmsshort_a-BloomFilters.o libralgorithmsshort_a-Contigs.o libralgorithmsshort_a-SequenceTree.o libralgorithmsshort_a-RUtils.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libralgorithmsshort.a g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 -ldl -lm make[4]: Leaving directory '/<>/RResolver' Making all in AdjList make[4]: Entering directory '/<>/AdjList' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 '/<>/AdjList' Making all in vendor make[4]: Entering directory '/<>/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/vendor' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/<>/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/vendor/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/<>/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/Unittest' make[4]: Entering directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' markdown README.md > README.html make[1]: Leaving directory '/<>' dh_auto_test make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/<>' Making check in bin make[2]: Entering directory '/<>/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/bin' Making check in doc make[2]: Entering directory '/<>/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/doc' Making check in Common make[2]: Entering directory '/<>/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Common' Making check in Graph make[2]: Entering directory '/<>/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Graph' Making check in DataLayer make[2]: Entering directory '/<>/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/DataLayer' Making check in DataBase make[2]: Entering directory '/<>/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/DataBase' Making check in FMIndex make[2]: Entering directory '/<>/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/FMIndex' Making check in Assembly make[2]: Entering directory '/<>/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Assembly' Making check in dialign make[2]: Entering directory '/<>/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/dialign' Making check in Align make[2]: Entering directory '/<>/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Align' Making check in ABYSS make[2]: Entering directory '/<>/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/ABYSS' Making check in Parallel make[2]: Entering directory '/<>/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Parallel' Making check in Bloom make[2]: Entering directory '/<>/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Bloom' Making check in BloomDBG make[2]: Entering directory '/<>/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/BloomDBG' Making check in Konnector make[2]: Entering directory '/<>/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Konnector' Making check in Consensus make[2]: Entering directory '/<>/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Consensus' Making check in DAssembler make[2]: Entering directory '/<>/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/DAssembler' Making check in DistanceEst make[2]: Entering directory '/<>/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/DistanceEst' Making check in KAligner make[2]: Entering directory '/<>/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/KAligner' Making check in Layout make[2]: Entering directory '/<>/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Layout' Making check in LogKmerCount make[2]: Entering directory '/<>/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/LogKmerCount' Making check in Map make[2]: Entering directory '/<>/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Map' Making check in MergePaths make[2]: Entering directory '/<>/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/MergePaths' Making check in Overlap make[2]: Entering directory '/<>/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Overlap' Making check in PairedDBG make[2]: Entering directory '/<>/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/<>/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/<>/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/<>/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/PopBubbles' Making check in Scaffold make[2]: Entering directory '/<>/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/<>/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/<>/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/kmerprint' Making check in FilterGraph make[2]: Entering directory '/<>/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/FilterGraph' Making check in GapFiller make[2]: Entering directory '/<>/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/GapFiller' Making check in Sealer make[2]: Entering directory '/<>/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/Sealer' Making check in RResolver make[2]: Entering directory '/<>/RResolver' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/RResolver' Making check in AdjList make[2]: Entering directory '/<>/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/AdjList' Making check in vendor make[2]: Entering directory '/<>/vendor' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/vendor' Making check in vendor/gtest-1.7.0 make[2]: Entering directory '/<>/vendor/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/<>/vendor/gtest-1.7.0' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -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 cru libgtest.a src/libgtest_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a rm -f libgtest_main.a ar cru libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest_main.a make[3]: Leaving directory '/<>/vendor/gtest-1.7.0' make[2]: Leaving directory '/<>/vendor/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/<>/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 '/<>/Unittest' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerTest.o Common/KmerTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/Sequence.o Common/Sequence.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/SAM.o Common/SAM.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -DSAM_SEQ_QUAL -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/common_sam_ssq-SAM.o `test -f 'Common/SAM.cc' || echo './'`Common/SAM.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o `test -f 'BloomDBG/CountingBloomFilterTest.cpp' || echo './'`BloomDBG/CountingBloomFilterTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/<> -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/<>/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o common_sam_ssq Common/common_sam_ssq-SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-Bsymbolic-functions -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 make[3]: Leaving directory '/<>/Unittest' make check-TESTS make[3]: Entering directory '/<>/Unittest' make[4]: Entering directory '/<>/Unittest' PASS: common_histogram PASS: common_kmer PASS: common_bitutil PASS: common_stringutil PASS: common_sequence PASS: common_KmerIterator PASS: common_sam PASS: common_sam_ssq PASS: BloomFilter PASS: Konnector_DBGBloom PASS: Konnector_DBGBloomAlgorithms PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_ExtendPath PASS: graph_DotIO PASS: graph_UndirectedGraph PASS: Konnector_konnector PASS: PairedDBG_KmerPair 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 PASS: DBG_LoadAlgorithm PASS: PairedDBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.3.5 ============================================================================ # TOTAL: 34 # PASS: 34 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/<>/Unittest' make[3]: Leaving directory '/<>/Unittest' make[2]: Leaving directory '/<>/Unittest' make[2]: Entering directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install --destdir=debian/tmp make -j4 install DESTDIR=/<>/abyss-2.3.5\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' Making install in bin make[3]: Entering directory '/<>/bin' make[4]: Entering directory '/<>/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/bin' make[3]: Leaving directory '/<>/bin' Making install in doc make[3]: Entering directory '/<>/doc' make[4]: Entering directory '/<>/doc' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/<>/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/<>/doc' make[3]: Leaving directory '/<>/doc' Making install in Common make[3]: Entering directory '/<>/Common' make[4]: Entering directory '/<>/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 '/<>/Common' make[3]: Leaving directory '/<>/Common' Making install in Graph make[3]: Entering directory '/<>/Graph' make[4]: Entering directory '/<>/Graph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Graph' make[3]: Leaving directory '/<>/Graph' Making install in DataLayer make[3]: Entering directory '/<>/DataLayer' make[4]: Entering directory '/<>/DataLayer' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/DataLayer' make[3]: Leaving directory '/<>/DataLayer' Making install in DataBase make[3]: Entering directory '/<>/DataBase' make[4]: Entering directory '/<>/DataBase' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/DataBase' make[3]: Leaving directory '/<>/DataBase' Making install in FMIndex make[3]: Entering directory '/<>/FMIndex' make[4]: Entering directory '/<>/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 '/<>/FMIndex' make[3]: Leaving directory '/<>/FMIndex' Making install in Assembly make[3]: Entering directory '/<>/Assembly' make[4]: Entering directory '/<>/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 '/<>/Assembly' make[3]: Leaving directory '/<>/Assembly' Making install in dialign make[3]: Entering directory '/<>/dialign' make[4]: Entering directory '/<>/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 '/<>/dialign' make[3]: Leaving directory '/<>/dialign' Making install in Align make[3]: Entering directory '/<>/Align' make[4]: Entering directory '/<>/Align' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Align' make[3]: Leaving directory '/<>/Align' Making install in ABYSS make[3]: Entering directory '/<>/ABYSS' make[4]: Entering directory '/<>/ABYSS' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/ABYSS' make[3]: Leaving directory '/<>/ABYSS' Making install in Parallel make[3]: Entering directory '/<>/Parallel' make[4]: Entering directory '/<>/Parallel' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Parallel' make[3]: Leaving directory '/<>/Parallel' Making install in Bloom make[3]: Entering directory '/<>/Bloom' make[4]: Entering directory '/<>/Bloom' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Bloom' make[3]: Leaving directory '/<>/Bloom' Making install in BloomDBG make[3]: Entering directory '/<>/BloomDBG' make[4]: Entering directory '/<>/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/BloomDBG' make[3]: Leaving directory '/<>/BloomDBG' Making install in Konnector make[3]: Entering directory '/<>/Konnector' make[4]: Entering directory '/<>/Konnector' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c konnector '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Konnector' make[3]: Leaving directory '/<>/Konnector' Making install in Consensus make[3]: Entering directory '/<>/Consensus' make[4]: Entering directory '/<>/Consensus' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Consensus '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Consensus' make[3]: Leaving directory '/<>/Consensus' Making install in DAssembler make[3]: Entering directory '/<>/DAssembler' make[4]: Entering directory '/<>/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/DAssembler' make[3]: Leaving directory '/<>/DAssembler' Making install in DistanceEst make[3]: Entering directory '/<>/DistanceEst' make[4]: Entering directory '/<>/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/DistanceEst' make[3]: Leaving directory '/<>/DistanceEst' Making install in KAligner make[3]: Entering directory '/<>/KAligner' make[4]: Entering directory '/<>/KAligner' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/KAligner' make[3]: Leaving directory '/<>/KAligner' Making install in Layout make[3]: Entering directory '/<>/Layout' make[4]: Entering directory '/<>/Layout' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Layout' make[3]: Leaving directory '/<>/Layout' Making install in LogKmerCount make[3]: Entering directory '/<>/LogKmerCount' make[4]: Entering directory '/<>/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/LogKmerCount' make[3]: Leaving directory '/<>/LogKmerCount' Making install in Map make[3]: Entering directory '/<>/Map' make[4]: Entering directory '/<>/Map' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Map' make[3]: Leaving directory '/<>/Map' Making install in MergePaths make[3]: Entering directory '/<>/MergePaths' make[4]: Entering directory '/<>/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/MergePaths' make[3]: Leaving directory '/<>/MergePaths' Making install in Overlap make[3]: Entering directory '/<>/Overlap' make[4]: Entering directory '/<>/Overlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Overlap' make[3]: Leaving directory '/<>/Overlap' Making install in PairedDBG make[3]: Entering directory '/<>/PairedDBG' make[4]: Entering directory '/<>/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/PairedDBG' make[3]: Leaving directory '/<>/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/<>/ParseAligns' make[4]: Entering directory '/<>/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/ParseAligns' make[3]: Leaving directory '/<>/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/<>/PathOverlap' make[4]: Entering directory '/<>/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/PathOverlap' make[3]: Leaving directory '/<>/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/<>/PopBubbles' make[4]: Entering directory '/<>/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/PopBubbles' make[3]: Leaving directory '/<>/PopBubbles' Making install in Scaffold make[3]: Entering directory '/<>/Scaffold' make[4]: Entering directory '/<>/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Scaffold' make[3]: Leaving directory '/<>/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/<>/SimpleGraph' make[4]: Entering directory '/<>/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/SimpleGraph' make[3]: Leaving directory '/<>/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/<>/kmerprint' make[4]: Entering directory '/<>/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 '/<>/kmerprint' make[3]: Leaving directory '/<>/kmerprint' Making install in FilterGraph make[3]: Entering directory '/<>/FilterGraph' make[4]: Entering directory '/<>/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/FilterGraph' make[3]: Leaving directory '/<>/FilterGraph' Making install in GapFiller make[3]: Entering directory '/<>/GapFiller' make[4]: Entering directory '/<>/GapFiller' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/GapFiller' make[3]: Leaving directory '/<>/GapFiller' Making install in Sealer make[3]: Entering directory '/<>/Sealer' make[4]: Entering directory '/<>/Sealer' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/Sealer' make[3]: Leaving directory '/<>/Sealer' Making install in RResolver make[3]: Entering directory '/<>/RResolver' make[4]: Entering directory '/<>/RResolver' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c abyss-rresolver-short '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/RResolver' make[3]: Leaving directory '/<>/RResolver' Making install in AdjList make[3]: Entering directory '/<>/AdjList' make[4]: Entering directory '/<>/AdjList' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/<>/debian/tmp/usr/bin' make[4]: Leaving directory '/<>/AdjList' make[3]: Leaving directory '/<>/AdjList' Making install in vendor make[3]: Entering directory '/<>/vendor' make[4]: Entering directory '/<>/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 '/<>/vendor' make[3]: Leaving directory '/<>/vendor' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/<>/vendor/gtest-1.7.0' make[4]: Entering directory '/<>/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 '/<>/vendor/gtest-1.7.0' make[3]: Leaving directory '/<>/vendor/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/<>/Unittest' make[4]: Entering directory '/<>/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 '/<>/Unittest' make[3]: Leaving directory '/<>/Unittest' make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/<>/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' 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 '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' 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 '/<>' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a debugedit: debian/abyss/usr/lib/abyss/abyss-scaffold: Unknown DWARF DW_FORM_0x1f20 004983180f990f9fb5660c0570d575e2e3de39eb debugedit: debian/abyss/usr/lib/abyss/abyss-mergepairs: Unknown DWARF DW_FORM_0x1f20 93f821cdd3d0cfaea6096b5047d4a518900d9c86 debugedit: debian/abyss/usr/lib/abyss/abyss-overlap: Unknown DWARF DW_FORM_0x1f21 eee326f8a4c538c6c9191a8278a207f3975e1101 debugedit: debian/abyss/usr/lib/abyss/logcounter: Unknown DWARF DW_FORM_0x1f21 8e3c540199ba19d734aaf2add8e0e942ddf8a8eb debugedit: debian/abyss/usr/lib/abyss/AdjList: Unknown DWARF DW_FORM_0x1f21 7268c91f12dbc3941d403c3e5f12744d522484e2 debugedit: debian/abyss/usr/lib/abyss/abyss-fixmate: Unknown DWARF DW_FORM_0x1f20 f51540693b7552a710c7a8d325ea9325392e498a debugedit: debian/abyss/usr/lib/abyss/PathOverlap: Unknown DWARF DW_FORM_0x1f20 defacf3470b01f279bb56bb28f37887119ae32d9 debugedit: debian/abyss/usr/lib/abyss/ABYSS-P: Unknown DWARF DW_FORM_0x1f20 2d1e8714b74f6e53939d50d2bd9b464215acf630 debugedit: debian/abyss/usr/lib/abyss/MergeContigs: Unknown DWARF DW_FORM_0x1f21 c0454423a4e2e6b69f2ae6165f655dd90fecf937 debugedit: debian/abyss/usr/lib/abyss/abyss-fixmate-ssq: Unknown DWARF DW_FORM_0x1f20 995f2db56bce2c1ff0e97131dfe9ac502d8c97fd debugedit: debian/abyss/usr/lib/abyss/abyss-gc: Unknown DWARF DW_FORM_0x1f20 b498d60477d6dd31b38d0afeb696d96066c5fe95 debugedit: debian/abyss/usr/lib/abyss/abyss-map-ssq: Unknown DWARF DW_FORM_0x1f21 31e0dcebb5376823a1677f20570c1c574afdc7b3 debugedit: debian/abyss/usr/lib/abyss/DAssembler: Unknown DWARF DW_FORM_0x1f20 d637aa13051e49de7a30afd730f9783febf70d39 debugedit: debian/abyss/usr/lib/abyss/MergePaths: Unknown DWARF DW_FORM_0x1f20 0713eb9ae5b1932e6dcf396aade3735a75335cca debugedit: debian/abyss/usr/lib/abyss/Overlap: Unknown DWARF DW_FORM_0x1f21 3a985e672ce7442481302387beb508033dd020e6 debugedit: debian/abyss/usr/lib/abyss/PathConsensus: Unknown DWARF DW_FORM_0x1f20 584ccb0b79da008216c173e993d185137ef74f9d debugedit: debian/abyss/usr/lib/abyss/abyss-bloom-dbg: Unknown DWARF DW_FORM_0x1f21 e85af307437f58bacb1efde62d30f7c7e87f1635 debugedit: debian/abyss/usr/lib/abyss/Consensus: Unknown DWARF DW_FORM_0x1f20 077c96b45fdda9d9c3de8d0b1eecb0d578e7f16b debugedit: debian/abyss/usr/lib/abyss/PopBubbles: Unknown DWARF DW_FORM_0x1f21 462e7bdd0b3caded90f679b97294bdf2e766c45d debugedit: debian/abyss/usr/lib/abyss/abyss-db-csv: Unknown DWARF DW_FORM_0x1f20 d061c1f19b5e186a054bb59abc146e3a7fae5bf6 debugedit: debian/abyss/usr/lib/abyss/DistanceEst: Unknown DWARF DW_FORM_0x1f20 469786a42225fb2d5c22ce038a4734b3accfe0c6 debugedit: debian/abyss/usr/lib/abyss/abyss-paired-dbg-mpi: Unknown DWARF DW_FORM_0x1f21 a2262bb059bd219e3ef2073d695ffa810c6dc5d0 debugedit: debian/abyss/usr/lib/abyss/ABYSS: Unknown DWARF DW_FORM_0x1f20 bb52d9c9db60f36a07e2779e530ecd5861c931b3 debugedit: debian/abyss/usr/lib/abyss/ParseAligns: Unknown DWARF DW_FORM_0x1f20 fecc6d780d0bea3ad5be36c6a6425cafc061bb34 debugedit: debian/abyss/usr/lib/abyss/abyss-fac: Unknown DWARF DW_FORM_0x1f21 7e7f8299528ef7c3cc1c7f3a0c10748a6b47b4fe debugedit: debian/abyss/usr/lib/abyss/abyss-rresolver-short: Unknown DWARF DW_FORM_0x1f20 1ae76d9bbf262daa55c5428f19b8d3b900661d9e debugedit: debian/abyss/usr/lib/abyss/SimpleGraph: Unknown DWARF DW_FORM_0x1f20 323ff81934b73e5ee3cb806b19fdd40853a20250 debugedit: debian/abyss/usr/lib/abyss/abyss-paired-dbg: Unknown DWARF DW_FORM_0x1f20 8c2ed6938f5dfe8aae4710b240cb40d8aac72ceb debugedit: debian/abyss/usr/lib/abyss/abyss-index: Unknown DWARF DW_FORM_0x1f20 944b02b1ff09b03dd7043286e7a5b446899dca1b debugedit: debian/abyss/usr/lib/abyss/KAligner: Unknown DWARF DW_FORM_0x1f20 71b65eb9c89b77b0d0e324b781327bd606ff69e6 debugedit: debian/abyss/usr/lib/abyss/abyss-align: Unknown DWARF DW_FORM_0x1f20 c7569ed0eb04ee505ffde398e9ed4b085ddbe2c8 debugedit: debian/abyss/usr/lib/abyss/abyss-gapfill: Unknown DWARF DW_FORM_0x1f21 7f11ccbaeb0fd989f4bd92cbc21c0fa86c5d912e debugedit: debian/abyss/usr/lib/abyss/abyss-layout: Unknown DWARF DW_FORM_0x1f20 bd4efd3073af1126e4ca55f98b5605e72818a9ac debugedit: debian/abyss/usr/lib/abyss/abyss-longseqdist: Unknown DWARF DW_FORM_0x1f20 28a560dc9179badd9f37e1547c363cc3a356739e debugedit: debian/abyss/usr/lib/abyss/abyss-tofastq: Unknown DWARF DW_FORM_0x1f20 ea4c7fce3fbbaba9a7aebc2c58b7a8fc6ab4bddf debugedit: debian/abyss/usr/lib/abyss/abyss-map: Unknown DWARF DW_FORM_0x1f21 c1005a0aefc16779108211daf9f9e3f178f19c2d debugedit: debian/abyss/usr/lib/abyss/abyss-todot: Unknown DWARF DW_FORM_0x1f20 8e189112a32973851c0705588c84111fb4b1d295 debugedit: debian/abyss/usr/lib/abyss/DistanceEst-ssq: Unknown DWARF DW_FORM_0x1f20 725d98d83bef380827d6338b993db0548eadda9a debugedit: debian/abyss/usr/lib/abyss/abyss-junction: Unknown DWARF DW_FORM_0x1f20 3a4c71f99812eef97a8f7728eca388cb3393dd4d debugedit: debian/abyss/usr/lib/abyss/konnector: Unknown DWARF DW_FORM_0x1f20 e5b3c00608c528e89b2fea9c0d634ce43a408bc4 debugedit: debian/abyss/usr/lib/abyss/abyss-filtergraph: Unknown DWARF DW_FORM_0x1f21 fa688278313c3a4ba6bc77fd59284df2251d2c54 debugedit: debian/abyss/usr/lib/abyss/abyss-sealer: Unknown DWARF DW_FORM_0x1f20 43b1cbe58272ca18cef974a6ab7b087ee1665b6a debugedit: debian/abyss/usr/lib/abyss/abyss-bloom: Unknown DWARF DW_FORM_0x1f21 48f0ff1ffe80c27740cb21ed5cc7a020ead3e157 debugedit: debian/abyss/usr/bin/abyss-fixmate: Unknown DWARF DW_FORM_0x1f20 f51540693b7552a710c7a8d325ea9325392e498a debugedit: debian/abyss/usr/bin/DistanceEst: Unknown DWARF DW_FORM_0x1f20 469786a42225fb2d5c22ce038a4734b3accfe0c6 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing abyss-dbgsym (in debian/.debhelper/abyss/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing abyss (in debian/abyss); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/abyss/DEBIAN/control, package abyss, directory debian/abyss pkgstripfiles: Truncating usr/share/doc/abyss/changelog.Debian.gz to topmost ten records pkgstripfiles: processing control file: debian/.debhelper/abyss/dbgsym-root/DEBIAN/control, package abyss-dbgsym, directory debian/.debhelper/abyss/dbgsym-root dpkg-deb: building package 'abyss-dbgsym' in 'debian/.debhelper/scratch-space/build-abyss/abyss-dbgsym_2.3.5+dfsg-1_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package abyss ... pkgstripfiles: No PNG files. dpkg-deb: building package 'abyss' in '../abyss_2.3.5+dfsg-1_amd64.deb'. Renaming abyss-dbgsym_2.3.5+dfsg-1_amd64.deb to abyss-dbgsym_2.3.5+dfsg-1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../abyss_2.3.5+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../abyss_2.3.5+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-05-14T23:21:07Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ abyss_2.3.5+dfsg-1_amd64.changes: --------------------------------- Format: 1.8 Date: Sat, 14 May 2022 14:19:36 +0200 Source: abyss Binary: abyss Built-For-Profiles: noudeb Architecture: amd64 Version: 2.3.5+dfsg-1 Distribution: kinetic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (2.3.5+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.6.1 (routine-update) * Add fix-privacy-breach.patch; this is to avoid pinging a badges server while reading the offline documentation. 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Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: abyss Binary: abyss abyss-dbgsym Architecture: amd64 Version: 2.3.5+dfsg-1 Checksums-Md5: 64de31d7c2ebccc6c247944bcfe59270 32035296 abyss-dbgsym_2.3.5+dfsg-1_amd64.ddeb cc3a4bd96f207806dc46c756045c96fe 3250900 abyss_2.3.5+dfsg-1_amd64.deb Checksums-Sha1: 5919c15d6db4eb547128c76655e20261b16b43dc 32035296 abyss-dbgsym_2.3.5+dfsg-1_amd64.ddeb ec774e0c4a2a14dea5d76c3e436ea192686ab608 3250900 abyss_2.3.5+dfsg-1_amd64.deb Checksums-Sha256: c78e89efc2ea767a2c39668bb75329995ad04f70bac890ef6ecfc2450c9be43d 32035296 abyss-dbgsym_2.3.5+dfsg-1_amd64.ddeb 9081e51fe56b21d15fc7f045a0aec56a1eaec6aba37c25c3bf1216535402ef42 3250900 abyss_2.3.5+dfsg-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Sat, 14 May 2022 23:21:06 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.118ubuntu5), autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-4ubuntu4), autotools-dev (= 20220109.1), base-files (= 12ubuntu5), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38-4ubuntu1), binutils-common (= 2.38-4ubuntu1), binutils-x86-64-linux-gnu (= 2.38-4ubuntu1), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-1ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8), debconf (= 1.5.79ubuntu1), debhelper (= 13.7.1ubuntu1), debianutils (= 5.7-0.2), debugedit (= 1:5.0-4build1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), dpkg (= 1.21.7ubuntu3), dpkg-dev (= 1.21.7ubuntu3), dwz (= 0.14-1build2), file (= 1:5.41-4), findutils (= 4.8.0-1ubuntu3), g++ (= 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(= 2.1.12-stable-5), libevent-dev (= 2.1.12-stable-5), libevent-extra-2.1-7 (= 2.1.12-stable-5), libevent-openssl-2.1-7 (= 2.1.12-stable-5), libevent-pthreads-2.1-7 (= 2.1.12-stable-5), libfabric1 (= 1.11.0-3), libffi8 (= 3.4.2-4), libfido2-1 (= 1.11.0-1), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-11-dev (= 11.3.0-1ubuntu1), libgcc-s1 (= 12.1.0-2ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu3), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgfortran-11-dev (= 11.3.0-1ubuntu1), libgfortran5 (= 12.1.0-2ubuntu1), libglib2.0-0 (= 2.72.1-1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgnutls30 (= 3.7.4-2ubuntu1), libgomp1 (= 12.1.0-2ubuntu1), libgpg-error0 (= 1.45-2), libgssapi-krb5-2 (= 1.19.2-2), libhogweed6 (= 3.7.3-1build2), libhtml-parser-perl (= 3.78-1), libhtml-tagset-perl (= 3.20-4), libhwloc-dev (= 2.7.1-1), libhwloc-plugins (= 2.7.1-1), libhwloc15 (= 2.7.1-1), libibverbs-dev (= 39.0-1), libibverbs1 (= 39.0-1), libicu-dev (= 71.1-3), libicu71 (= 71.1-3), libidn2-0 (= 2.3.2-2build1), libisl23 (= 0.24-2build1), libitm1 (= 12.1.0-2ubuntu1), libjs-jquery (= 3.6.0+dfsg+~3.5.13-1), libjs-jquery-ui (= 1.13.1+dfsg-1), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-2ubuntu3), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), libldap-2.5-0 (= 2.5.11+dfsg-1~exp1ubuntu3), liblocale-gettext-perl (= 1.07-4build3), liblsan0 (= 12.1.0-2ubuntu1), libltdl-dev (= 2.4.7-4), libltdl7 (= 2.4.7-4), liblz4-1 (= 1.9.3-2build2), liblzma5 (= 5.2.5-2ubuntu1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-1build1), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libnettle8 (= 3.7.3-1build2), libnghttp2-14 (= 1.47.0-1), libnl-3-200 (= 3.5.0-0.1), libnl-3-dev (= 3.5.0-0.1), libnl-route-3-200 (= 3.5.0-0.1), libnl-route-3-dev (= 3.5.0-0.1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libnuma-dev (= 2.0.14-3ubuntu2), libnuma1 (= 2.0.14-3ubuntu2), libopenmpi-dev (= 4.1.3-2ubuntu1), libopenmpi3 (= 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0.9.6-2build1), libssl3 (= 3.0.3-0ubuntu1), libstdc++-11-dev (= 11.3.0-1ubuntu1), libstdc++6 (= 12.1.0-2ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.11-0ubuntu3.1), libtasn1-6 (= 4.18.0-4build1), libtext-markdown-perl (= 1.000031-3), libtext-multimarkdown-perl (= 1.000035-2), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtool (= 2.4.7-4), libtsan0 (= 11.3.0-1ubuntu1), libubsan1 (= 12.1.0-2ubuntu1), libuchardet0 (= 0.0.7-1build2), libucx0 (= 1.12.1-1), libudev1 (= 249.11-0ubuntu3.1), libunistring2 (= 1.0-1), liburi-perl (= 5.10-1), libuuid1 (= 2.38-4ubuntu1), libx11-6 (= 2:1.7.5-1), libx11-data (= 2:1.7.5-1), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.14-3ubuntu3), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxml2 (= 2.9.14+dfsg-1), libxnvctrl0 (= 510.47.03-0ubuntu1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.15.0-28.29), login (= 1:4.8.1-2ubuntu2), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 25), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), ocl-icd-libopencl1 (= 2.2.14-3), openmpi-bin (= 4.1.3-2ubuntu1), openmpi-common (= 4.1.3-2ubuntu1), openssh-client (= 1:9.0p1-1), passwd (= 1:4.8.1-2ubuntu2), patch (= 2.7.6-7build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), pkg-config (= 0.29.2-1ubuntu3), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.5-2ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1652530776" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ abyss_2.3.5+dfsg-1_amd64.deb ---------------------------- new Debian package, version 2.0. size 3250900 bytes: control archive=2619 bytes. 791 bytes, 15 lines control 4713 bytes, 75 lines md5sums Package: abyss Version: 2.3.5+dfsg-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 9673 Depends: make, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libopenmpi3 (>= 4.1.3), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 12), perl:any, bsdextrautils, openmpi-common, openmpi-bin Section: science Priority: optional Homepage: https://github.com/bcgsc/abyss Description: de novo, parallel, sequence assembler for short reads ABySS is a de novo, parallel, sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread. drwxr-xr-x root/root 0 2022-05-14 12:19 ./ drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/ drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/bin/ -rwxr-xr-x root/root 141816 2022-05-14 12:19 ./usr/bin/DistanceEst -rwxr-xr-x root/root 129504 2022-05-14 12:19 ./usr/bin/abyss-fixmate -rwxr-xr-x root/root 23148 2022-05-14 12:19 ./usr/bin/abyss-pe drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/lib/ drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/lib/abyss/ -rwxr-xr-x root/root 264720 2022-05-14 12:19 ./usr/lib/abyss/ABYSS -rwxr-xr-x root/root 313872 2022-05-14 12:19 ./usr/lib/abyss/ABYSS-P -rwxr-xr-x root/root 174576 2022-05-14 12:19 ./usr/lib/abyss/AdjList -rwxr-xr-x root/root 76264 2022-05-14 12:19 ./usr/lib/abyss/Consensus -rwxr-xr-x root/root 104952 2022-05-14 12:19 ./usr/lib/abyss/DAssembler -rwxr-xr-x root/root 141816 2022-05-14 12:19 ./usr/lib/abyss/DistanceEst -rwxr-xr-x root/root 145912 2022-05-14 12:19 ./usr/lib/abyss/DistanceEst-ssq -rwxr-xr-x root/root 186872 2022-05-14 12:19 ./usr/lib/abyss/KAligner -rwxr-xr-x root/root 223744 2022-05-14 12:19 ./usr/lib/abyss/MergeContigs -rwxr-xr-x root/root 190952 2022-05-14 12:19 ./usr/lib/abyss/MergePaths -rwxr-xr-x root/root 190968 2022-05-14 12:19 ./usr/lib/abyss/Overlap -rwxr-xr-x root/root 96728 2022-05-14 12:19 ./usr/lib/abyss/ParseAligns -rwxr-xr-x root/root 342520 2022-05-14 12:19 ./usr/lib/abyss/PathConsensus -rwxr-xr-x root/root 174552 2022-05-14 12:19 ./usr/lib/abyss/PathOverlap -rwxr-xr-x root/root 190968 2022-05-14 12:19 ./usr/lib/abyss/PopBubbles -rwxr-xr-x root/root 174584 2022-05-14 12:19 ./usr/lib/abyss/SimpleGraph -rwxr-xr-x root/root 186856 2022-05-14 12:19 ./usr/lib/abyss/abyss-align -rwxr-xr-x root/root 346720 2022-05-14 12:19 ./usr/lib/abyss/abyss-bloom -rwxr-xr-x root/root 367168 2022-05-14 12:19 ./usr/lib/abyss/abyss-bloom-dbg -rwxr-xr-x root/root 6491 2022-05-14 12:19 ./usr/lib/abyss/abyss-bloom-dist.mk -rwxr-xr-x root/root 1135 2022-05-14 12:19 ./usr/lib/abyss/abyss-bowtie -rwxr-xr-x root/root 1192 2022-05-14 12:19 ./usr/lib/abyss/abyss-bowtie2 -rwxr-xr-x root/root 1208 2022-05-14 12:19 ./usr/lib/abyss/abyss-bwa -rwxr-xr-x root/root 1454 2022-05-14 12:19 ./usr/lib/abyss/abyss-bwamem -rwxr-xr-x root/root 1362 2022-05-14 12:19 ./usr/lib/abyss/abyss-bwasw -rwxr-xr-x root/root 68056 2022-05-14 12:19 ./usr/lib/abyss/abyss-db-csv -rwxr-xr-x root/root 703 2022-05-14 12:19 ./usr/lib/abyss/abyss-db-txt -rwxr-xr-x root/root 2739 2022-05-14 12:19 ./usr/lib/abyss/abyss-dida -rwxr-xr-x root/root 80368 2022-05-14 12:19 ./usr/lib/abyss/abyss-fac -rwxr-xr-x root/root 2058 2022-05-14 12:19 ./usr/lib/abyss/abyss-fatoagp -rwxr-xr-x root/root 170488 2022-05-14 12:19 ./usr/lib/abyss/abyss-filtergraph -rwxr-xr-x root/root 129504 2022-05-14 12:19 ./usr/lib/abyss/abyss-fixmate -rwxr-xr-x root/root 129504 2022-05-14 12:19 ./usr/lib/abyss/abyss-fixmate-ssq -rwxr-xr-x root/root 100856 2022-05-14 12:19 ./usr/lib/abyss/abyss-gapfill -rwxr-xr-x root/root 84440 2022-05-14 12:19 ./usr/lib/abyss/abyss-gc -rwxr-xr-x root/root 88544 2022-05-14 12:19 ./usr/lib/abyss/abyss-index -rwxr-xr-x root/root 92640 2022-05-14 12:19 ./usr/lib/abyss/abyss-junction -rwxr-xr-x root/root 39 2022-05-14 12:19 ./usr/lib/abyss/abyss-kaligner -rwxr-xr-x root/root 129504 2022-05-14 12:19 ./usr/lib/abyss/abyss-layout -rwxr-xr-x root/root 92648 2022-05-14 12:19 ./usr/lib/abyss/abyss-longseqdist -rwxr-xr-x root/root 178672 2022-05-14 12:19 ./usr/lib/abyss/abyss-map -rwxr-xr-x root/root 182768 2022-05-14 12:19 ./usr/lib/abyss/abyss-map-ssq -rwxr-xr-x root/root 84480 2022-05-14 12:19 ./usr/lib/abyss/abyss-mergepairs -rwxr-xr-x root/root 195072 2022-05-14 12:19 ./usr/lib/abyss/abyss-overlap -rwxr-xr-x root/root 285208 2022-05-14 12:19 ./usr/lib/abyss/abyss-paired-dbg -rwxr-xr-x root/root 326160 2022-05-14 12:19 ./usr/lib/abyss/abyss-paired-dbg-mpi -rwxr-xr-x root/root 23148 2022-05-14 12:19 ./usr/lib/abyss/abyss-pe -rwxr-xr-x root/root 555632 2022-05-14 12:19 ./usr/lib/abyss/abyss-rresolver-short -rwxr-xr-x root/root 4501 2022-05-14 12:19 ./usr/lib/abyss/abyss-samtoafg -rwxr-xr-x root/root 236016 2022-05-14 12:19 ./usr/lib/abyss/abyss-scaffold -rwxr-xr-x root/root 223824 2022-05-14 12:19 ./usr/lib/abyss/abyss-sealer -rwxr-xr-x root/root 671 2022-05-14 12:19 ./usr/lib/abyss/abyss-stack-size -rwxr-xr-x root/root 209 2022-05-14 12:19 ./usr/lib/abyss/abyss-tabtomd -rwxr-xr-x root/root 162272 2022-05-14 12:19 ./usr/lib/abyss/abyss-todot -rwxr-xr-x root/root 63984 2022-05-14 12:19 ./usr/lib/abyss/abyss-tofastq -rwxr-xr-x root/root 244336 2022-05-14 12:19 ./usr/lib/abyss/konnector -rwxr-xr-x root/root 76280 2022-05-14 12:19 ./usr/lib/abyss/logcounter drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/share/ drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/share/doc-base/ -rw-r--r-- root/root 226 2022-05-14 12:19 ./usr/share/doc-base/abyss.abyss-flowcharts drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/share/doc/abyss/ -rw-r--r-- root/root 556 2022-05-14 12:19 ./usr/share/doc/abyss/CITATION.bib -rw-r--r-- root/root 1861 2022-05-14 12:19 ./usr/share/doc/abyss/CITATION.md -rw-r--r-- root/root 32008 2022-05-14 12:19 ./usr/share/doc/abyss/README.html -rw-r--r-- root/root 9507 2022-05-14 12:19 ./usr/share/doc/abyss/README.md.gz -rw-r--r-- root/root 182 2022-05-14 12:19 ./usr/share/doc/abyss/README.test -rw-r--r-- root/root 1343 2022-05-14 12:19 ./usr/share/doc/abyss/changelog.Debian.gz -rw-r--r-- root/root 7171 2022-05-14 12:19 ./usr/share/doc/abyss/copyright -rw-r--r-- root/root 66778 2022-05-14 12:19 ./usr/share/doc/abyss/flowchart.pdf.gz -rw-r--r-- root/root 22664 2022-05-14 12:19 ./usr/share/doc/abyss/flowchart_simplified.pdf.gz -rw-r--r-- root/root 677 2022-05-14 12:19 ./usr/share/doc/abyss/run-unit-test drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/share/doc/abyss/test-data/ -rw-r--r-- root/root 743013 2022-05-14 12:19 ./usr/share/doc/abyss/test-data/reads1.fastq.gz -rw-r--r-- root/root 743377 2022-05-14 12:19 ./usr/share/doc/abyss/test-data/reads2.fastq.gz drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/share/man/ drwxr-xr-x root/root 0 2022-05-14 12:19 ./usr/share/man/man1/ -rw-r--r-- root/root 1020 2022-05-14 12:19 ./usr/share/man/man1/DistanceEst.1.gz -rw-r--r-- root/root 787 2022-05-14 12:19 ./usr/share/man/man1/abyss-fixmate.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 830984 Build-Time: 247 Distribution: kinetic-proposed Host Architecture: amd64 Install-Time: 13 Job: abyss_2.3.5+dfsg-1.dsc Machine Architecture: amd64 Package: abyss Package-Time: 261 Source-Version: 2.3.5+dfsg-1 Space: 830984 Status: successful Version: 2.3.5+dfsg-1 -------------------------------------------------------------------------------- Finished at 2022-05-14T23:21:07Z Build needed 00:04:21, 830984k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23747339 Scanning for processes to kill in build PACKAGEBUILD-23747339