I: pbuilder: network access will be disabled during build I: Current time: Fri May 5 19:17:27 +14 2023 I: pbuilder-time-stamp: 1683263847 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [abyss_2.3.5+dfsg-2.dsc] I: copying [./abyss_2.3.5+dfsg.orig.tar.xz] I: copying [./abyss_2.3.5+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Oct 23 01:36:18 2022 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./abyss_2.3.5+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting abyss in abyss-2.3.5+dfsg dpkg-source: info: unpacking abyss_2.3.5+dfsg.orig.tar.xz dpkg-source: info: unpacking abyss_2.3.5+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying fix-privacy-breach.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1880974/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 5 19:18 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1880974/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1880974/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=3b94cc359e7f474d956d401e301f0bcc LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1880974 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.9Fgzdmb5/pbuilderrc_3knJ --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9Fgzdmb5/b2 --logfile b2/build.log --extrapackages usrmerge abyss_2.3.5+dfsg-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 May 5 19:18 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/1880974/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libsqlite3-dev, pkg-config, help2man, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libboost-graph-dev; however: Package libboost-graph-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev; however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however: Package libsparsehash-dev is not installed. pbuilder-satisfydepends-dummy depends on libtext-multimarkdown-perl; however: Package libtext-multimarkdown-perl is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran-12{a} groff-base{a} help2man{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-graph-dev{a} libboost-graph1.74-dev{a} libboost-graph1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-test1.74-dev{a} libboost-test1.74.0{a} libboost1.74-dev{a} libbsd0{a} libcbor0.8{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-12-dev{a} libgfortran5{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu-dev{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmunge2{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} libregexp-ipv6-perl{a} libsparsehash-dev{a} libsqlite3-dev{a} libsub-override-perl{a} libtext-markdown-perl{a} libtext-multimarkdown-perl{a} libtool{a} libuchardet0{a} libucx0{a} liburi-perl{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} m4{a} man-db{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libhttp-message-perl libmail-sendmail-perl lynx wget xauth 0 packages upgraded, 108 newly installed, 0 to remove and 0 not upgraded. Need to get 71.7 MB of archives. After unpacking 414 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2 [988 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libgfortran-12-dev amd64 12.2.0-14 [834 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 gfortran-12 amd64 12.2.0-14 [10.2 MB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74.0 amd64 1.74.0+ds1-20 [487 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libboost-graph1.74.0 amd64 1.74.0+ds1-20 [301 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74-dev amd64 1.74.0+ds1-20 [558 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libboost-serialization1.74.0 amd64 1.74.0+ds1-20 [318 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libboost-serialization1.74-dev amd64 1.74.0+ds1-20 [359 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libboost-test1.74.0 amd64 1.74.0+ds1-20 [453 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libboost-test1.74-dev amd64 1.74.0+ds1-20 [526 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libboost-graph1.74-dev amd64 1.74.0+ds1-20 [1480 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libboost-graph-dev amd64 1.74.0.3 [4436 B] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libevent-2.1-7 amd64 2.1.12-stable-8 [180 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-8 [107 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-8 [60.6 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libevent-dev amd64 2.1.12-stable-8 [305 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 70 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libnuma-dev amd64 2.0.16-1 [35.0 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libltdl7 amd64 2.4.7-5 [393 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libltdl-dev amd64 2.4.7-5 [164 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libhwloc-dev amd64 2.9.0-1 [241 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-1 [13.3 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libnl-3-dev amd64 3.7.0-0.2+b1 [104 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-dev amd64 3.7.0-0.2+b1 [203 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libibverbs-dev amd64 44.0-2 [633 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libpmix-dev amd64 4.2.2-1+b1 [902 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libopenmpi-dev amd64 4.1.4-3+b1 [970 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-dev amd64 3.40.1-2 [1025 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libtext-markdown-perl all 1.000031-4 [32.1 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libtext-multimarkdown-perl all 1.000035-3 [28.5 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Fetched 71.7 MB in 5s (15.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. 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Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../009-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../011-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../012-libedit2_3.1-20221030-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:amd64. Preparing to unpack .../013-libcbor0.8_0.8.0-2+b1_amd64.deb ... Unpacking libcbor0.8:amd64 (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../014-libfido2-1_1.12.0-2+b1_amd64.deb ... Unpacking libfido2-1:amd64 (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../015-openssh-client_1%3a9.2p1-2_amd64.deb ... Unpacking openssh-client (1:9.2p1-2) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../018-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../019-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../020-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../021-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../022-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../023-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../024-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../025-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../026-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../027-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../028-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../029-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../030-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../031-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../032-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../033-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../034-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../035-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../036-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Selecting previously unselected package libgfortran-12-dev:amd64. Preparing to unpack .../037-libgfortran-12-dev_12.2.0-14_amd64.deb ... Unpacking libgfortran-12-dev:amd64 (12.2.0-14) ... Selecting previously unselected package gfortran-12. Preparing to unpack .../038-gfortran-12_12.2.0-14_amd64.deb ... Unpacking gfortran-12 (12.2.0-14) ... Selecting previously unselected package help2man. Preparing to unpack .../039-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../040-libnl-3-200_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-3-200:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../041-libnl-route-3-200_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../042-libibverbs1_44.0-2_amd64.deb ... Unpacking libibverbs1:amd64 (44.0-2) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../043-ibverbs-providers_44.0-2_amd64.deb ... Unpacking ibverbs-providers:amd64 (44.0-2) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../044-icu-devtools_72.1-3_amd64.deb ... Unpacking icu-devtools (72.1-3) ... Selecting previously unselected package libboost1.74-dev:amd64. Preparing to unpack .../045-libboost1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-regex1.74.0:amd64. Preparing to unpack .../046-libboost-regex1.74.0_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-regex1.74.0:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-graph1.74.0:amd64. Preparing to unpack .../047-libboost-graph1.74.0_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-graph1.74.0:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libicu-dev:amd64. Preparing to unpack .../048-libicu-dev_72.1-3_amd64.deb ... Unpacking libicu-dev:amd64 (72.1-3) ... Selecting previously unselected package libboost-regex1.74-dev:amd64. Preparing to unpack .../049-libboost-regex1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-regex1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-serialization1.74.0:amd64. Preparing to unpack .../050-libboost-serialization1.74.0_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-serialization1.74.0:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-serialization1.74-dev:amd64. Preparing to unpack .../051-libboost-serialization1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-serialization1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-test1.74.0:amd64. Preparing to unpack .../052-libboost-test1.74.0_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-test1.74.0:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-test1.74-dev:amd64. Preparing to unpack .../053-libboost-test1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-test1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-graph1.74-dev:amd64. Preparing to unpack .../054-libboost-graph1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-graph1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-graph-dev:amd64. Preparing to unpack .../055-libboost-graph-dev_1.74.0.3_amd64.deb ... Unpacking libboost-graph-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libevent-2.1-7:amd64. Preparing to unpack .../056-libevent-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-core-2.1-7:amd64. Preparing to unpack .../057-libevent-core-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-extra-2.1-7:amd64. Preparing to unpack .../058-libevent-extra-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-extra-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-pthreads-2.1-7:amd64. Preparing to unpack .../059-libevent-pthreads-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-openssl-2.1-7:amd64. Preparing to unpack .../060-libevent-openssl-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-openssl-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../061-libevent-dev_2.1.12-stable-8_amd64.deb ... Unpacking libevent-dev (2.1.12-stable-8) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../062-libpsm-infinipath1_3.3+20.604758e7-6.2_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.2) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../063-libnuma1_2.0.16-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.16-1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../064-libpsm2-2_11.2.185-2_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../065-librdmacm1_44.0-2_amd64.deb ... Unpacking librdmacm1:amd64 (44.0-2) ... Selecting previously unselected package libfabric1:amd64. Preparing to unpack .../066-libfabric1_1.17.0-3_amd64.deb ... Unpacking libfabric1:amd64 (1.17.0-3) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../067-libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) ... Selecting previously unselected package libregexp-ipv6-perl. Preparing to unpack .../068-libregexp-ipv6-perl_0.03-3_all.deb ... Unpacking libregexp-ipv6-perl (0.03-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../069-liburi-perl_5.17-1_all.deb ... Unpacking liburi-perl (5.17-1) ... Selecting previously unselected package libhtml-parser-perl:amd64. Preparing to unpack .../070-libhtml-parser-perl_3.81-1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.81-1) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../071-libhwloc15_2.9.0-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.9.0-1) ... Selecting previously unselected package libnuma-dev:amd64. Preparing to unpack .../072-libnuma-dev_2.0.16-1_amd64.deb ... Unpacking libnuma-dev:amd64 (2.0.16-1) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../073-libltdl7_2.4.7-5_amd64.deb ... Unpacking libltdl7:amd64 (2.4.7-5) ... Selecting previously unselected package libltdl-dev:amd64. Preparing to unpack .../074-libltdl-dev_2.4.7-5_amd64.deb ... Unpacking libltdl-dev:amd64 (2.4.7-5) ... Selecting previously unselected package libhwloc-dev:amd64. Preparing to unpack .../075-libhwloc-dev_2.9.0-1_amd64.deb ... Unpacking libhwloc-dev:amd64 (2.9.0-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../076-libpciaccess0_0.17-2_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-2) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../077-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../078-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../079-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../080-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../081-libx11-6_2%3a1.8.4-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.4-2) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../082-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../083-libxnvctrl0_525.85.05-1_amd64.deb ... Unpacking libxnvctrl0:amd64 (525.85.05-1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../084-ocl-icd-libopencl1_2.3.1-1_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.3.1-1) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../085-libhwloc-plugins_2.9.0-1_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.9.0-1) ... Selecting previously unselected package libnl-3-dev:amd64. Preparing to unpack .../086-libnl-3-dev_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-3-dev:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-dev:amd64. Preparing to unpack .../087-libnl-route-3-dev_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-route-3-dev:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs-dev:amd64. 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Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../100-libpkgconf3_1.8.1-1_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-1) ... Selecting previously unselected package libsparsehash-dev. Preparing to unpack .../101-libsparsehash-dev_2.0.3-2_all.deb ... Unpacking libsparsehash-dev (2.0.3-2) ... Selecting previously unselected package libsqlite3-dev:amd64. Preparing to unpack .../102-libsqlite3-dev_3.40.1-2_amd64.deb ... Unpacking libsqlite3-dev:amd64 (3.40.1-2) ... Selecting previously unselected package libtext-markdown-perl. Preparing to unpack .../103-libtext-markdown-perl_1.000031-4_all.deb ... Unpacking libtext-markdown-perl (1.000031-4) ... Selecting previously unselected package libtext-multimarkdown-perl. Preparing to unpack .../104-libtext-multimarkdown-perl_1.000035-3_all.deb ... Unpacking libtext-multimarkdown-perl (1.000035-3) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../105-pkgconf-bin_1.8.1-1_amd64.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../106-pkgconf_1.8.1-1_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-1) ... Selecting previously unselected package pkg-config:amd64. Preparing to unpack .../107-pkg-config_1.8.1-1_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libtext-markdown-perl (1.000031-4) ... Setting up libpciaccess0:amd64 (0.17-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libcbor0.8:amd64 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libboost-test1.74.0:amd64 (1.74.0+ds1-20) ... Setting up libsqlite3-dev:amd64 (3.40.1-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libboost-regex1.74.0:amd64 (1.74.0+ds1-20) ... Setting up libhwloc15:amd64 (2.9.0-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libevent-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libboost-graph1.74.0:amd64 (1.74.0+ds1-20) ... Setting up autopoint (0.21-12) ... Setting up icu-devtools (72.1-3) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libltdl7:amd64 (2.4.7-5) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libboost-serialization1.74.0:amd64 (1.74.0+ds1-20) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libnuma1:amd64 (2.0.16-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.1-1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.4-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.12.0-2+b1) ... Setting up libboost-test1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libicu-dev:amd64 (72.1-3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up liburi-perl (5.17-1) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... 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 libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libevent-openssl-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libgfortran-12-dev:amd64 (12.2.0-14) ... Setting up pkgconf:amd64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.16-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.4.7-5) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up pkg-config:amd64 (1.8.1-1) ... Setting up libboost-serialization1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libboost-regex1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libnl-3-dev:amd64 (3.7.0-0.2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libhwloc-dev:amd64 (2.9.0-1) ... Setting up libtext-multimarkdown-perl (1.000035-3) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:amd64 (525.85.05-1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.2+b1) ... Setting up libboost-graph1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up libboost-graph-dev:amd64 (1.74.0.3) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up debhelper (13.11.4) ... Setting up libibverbs-dev:amd64 (44.0-2) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up libpmix2:amd64 (4.2.2-1+b1) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up libpmix-dev:amd64 (4.2.2-1+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... 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 (4.1.4-3+b1) ... 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 Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/1880974/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/1880974/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/abyss-2.3.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../abyss_2.3.5+dfsg-2_source.changes dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.3.5+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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 '/build/abyss-2.3.5+dfsg' 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 '2222' is supported by ustar format... yes checking whether GID '2222' 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 '/build/abyss-2.3.5+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-2.3.5+dfsg' dh_auto_build make -j15 make[2]: Entering directory '/build/abyss-2.3.5+dfsg' make all-recursive make[3]: Entering directory '/build/abyss-2.3.5+dfsg' Making all in bin make[4]: Entering directory '/build/abyss-2.3.5+dfsg/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/bin' Making all in doc make[4]: Entering directory '/build/abyss-2.3.5+dfsg/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/doc' Making all in Common make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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 '/build/abyss-2.3.5+dfsg/Common' Making all in Graph make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Graph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L. -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Graph' Making all in DataLayer make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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 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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-2.3.5+dfsg/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/FMIndex' Making all in Assembly make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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 '/build/abyss-2.3.5+dfsg/Assembly' Making all in dialign make[4]: Entering directory '/build/abyss-2.3.5+dfsg/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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, | ^~~~~~~~~~~ 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, | ^~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~ 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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/dialign' Making all in Align make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Align' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Align' Making all in ABYSS make[4]: Entering directory '/build/abyss-2.3.5+dfsg/ABYSS' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/ABYSS' Making all in Parallel make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Parallel' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Parallel' Making all in Bloom make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Bloom' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/abyss-2.3.5+dfsg/BloomDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Konnector' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Konnector' Making all in Consensus make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Consensus' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Consensus' Making all in DAssembler make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DAssembler' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DistanceEst' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-2.3.5+dfsg/KAligner' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/KAligner' Making all in Layout make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Layout' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/abyss-2.3.5+dfsg/LogKmerCount' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/LogKmerCount' Making all in Map make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Map' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Map' Making all in MergePaths make[4]: Entering directory '/build/abyss-2.3.5+dfsg/MergePaths' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/MergePaths' Making all in Overlap make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Overlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PairedDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/abyss-2.3.5+dfsg/ParseAligns' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PathOverlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PopBubbles' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Scaffold' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/abyss-2.3.5+dfsg/SimpleGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/abyss-2.3.5+dfsg/kmerprint' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/abyss-2.3.5+dfsg/FilterGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/abyss-2.3.5+dfsg/GapFiller' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/GapFiller' Making all in Sealer make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Sealer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Sealer' Making all in RResolver make[4]: Entering directory '/build/abyss-2.3.5+dfsg/RResolver' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -pthread -o abyss-rresolver-short abyss_rresolver_short-RResolverShort.o abyss_rresolver_short-Contigs.o ../DataLayer/libdatalayer.a ../Common/libcommon.a libralgorithmsshort.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/RResolver' Making all in AdjList make[4]: Entering directory '/build/abyss-2.3.5+dfsg/AdjList' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/AdjList' Making all in vendor make[4]: Entering directory '/build/abyss-2.3.5+dfsg/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/vendor' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-2.3.5+dfsg' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg' make[2]: Leaving directory '/build/abyss-2.3.5+dfsg' markdown README.md > README.html make[1]: Leaving directory '/build/abyss-2.3.5+dfsg' dh_auto_test make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[1]: Entering directory '/build/abyss-2.3.5+dfsg' Making check in bin make[2]: Entering directory '/build/abyss-2.3.5+dfsg/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/bin' Making check in doc make[2]: Entering directory '/build/abyss-2.3.5+dfsg/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/doc' Making check in Common make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Common' Making check in Graph make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Graph' Making check in DataLayer make[2]: Entering directory '/build/abyss-2.3.5+dfsg/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/DataLayer' Making check in DataBase make[2]: Entering directory '/build/abyss-2.3.5+dfsg/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/DataBase' Making check in FMIndex make[2]: Entering directory '/build/abyss-2.3.5+dfsg/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/FMIndex' Making check in Assembly make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Assembly' Making check in dialign make[2]: Entering directory '/build/abyss-2.3.5+dfsg/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/dialign' Making check in Align make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Align' Making check in ABYSS make[2]: Entering directory '/build/abyss-2.3.5+dfsg/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/ABYSS' Making check in Parallel make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Parallel' Making check in Bloom make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Bloom' Making check in BloomDBG make[2]: Entering directory '/build/abyss-2.3.5+dfsg/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/BloomDBG' Making check in Konnector make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Konnector' Making check in Consensus make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Consensus' Making check in DAssembler make[2]: Entering directory '/build/abyss-2.3.5+dfsg/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/abyss-2.3.5+dfsg/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/abyss-2.3.5+dfsg/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/KAligner' Making check in Layout make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/abyss-2.3.5+dfsg/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/LogKmerCount' Making check in Map make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Map' Making check in MergePaths make[2]: Entering directory '/build/abyss-2.3.5+dfsg/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/MergePaths' Making check in Overlap make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Overlap' Making check in PairedDBG make[2]: Entering directory '/build/abyss-2.3.5+dfsg/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/build/abyss-2.3.5+dfsg/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/abyss-2.3.5+dfsg/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/abyss-2.3.5+dfsg/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/abyss-2.3.5+dfsg/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/abyss-2.3.5+dfsg/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/abyss-2.3.5+dfsg/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/abyss-2.3.5+dfsg/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/GapFiller' Making check in Sealer make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Sealer' Making check in RResolver make[2]: Entering directory '/build/abyss-2.3.5+dfsg/RResolver' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/RResolver' Making check in AdjList make[2]: Entering directory '/build/abyss-2.3.5+dfsg/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/AdjList' Making check in vendor make[2]: Entering directory '/build/abyss-2.3.5+dfsg/vendor' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/vendor' Making check in vendor/gtest-1.7.0 make[2]: Entering directory '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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 '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/abyss-2.3.5+dfsg/Unittest' make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam common_sam_ssq BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_CountingBloomFilter BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Unittest' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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/build/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -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=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam_ssq Common/common_sam_ssq-SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Unittest' make check-TESTS make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Unittest' PASS: common_stringutil PASS: common_histogram PASS: common_bitutil PASS: common_kmer PASS: common_sequence PASS: common_KmerIterator PASS: common_sam PASS: common_sam_ssq PASS: BloomFilter PASS: Konnector_DBGBloomAlgorithms PASS: Konnector_DBGBloom PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_DotIO PASS: graph_ExtendPath PASS: Konnector_konnector PASS: graph_UndirectedGraph PASS: PairedDBG_KmerPair PASS: PairedDBG_BranchRecord PASS: PairedDBG_Dinuc PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_RollingHash 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 '/build/abyss-2.3.5+dfsg/Unittest' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Unittest' make[2]: Leaving directory '/build/abyss-2.3.5+dfsg/Unittest' make[2]: Entering directory '/build/abyss-2.3.5+dfsg' make[2]: Leaving directory '/build/abyss-2.3.5+dfsg' make[1]: Leaving directory '/build/abyss-2.3.5+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-2.3.5+dfsg' dh_auto_install --destdir=debian/tmp make -j15 install DESTDIR=/build/abyss-2.3.5\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-2.3.5+dfsg' Making install in bin make[3]: Entering directory '/build/abyss-2.3.5+dfsg/bin' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/bin' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/bin' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/bin' Making install in doc make[3]: Entering directory '/build/abyss-2.3.5+dfsg/doc' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/doc' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/doc' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/doc' Making install in Common make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Common' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Common' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Common' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Common' Making install in Graph make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Graph' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Graph' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Graph' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Graph' Making install in DataLayer make[3]: Entering directory '/build/abyss-2.3.5+dfsg/DataLayer' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DataLayer' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DataLayer' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/DataLayer' Making install in DataBase make[3]: Entering directory '/build/abyss-2.3.5+dfsg/DataBase' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DataBase' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-db-csv '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DataBase' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/DataBase' Making install in FMIndex make[3]: Entering directory '/build/abyss-2.3.5+dfsg/FMIndex' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/FMIndex' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/FMIndex' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/FMIndex' Making install in Assembly make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Assembly' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Assembly' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Assembly' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Assembly' Making install in dialign make[3]: Entering directory '/build/abyss-2.3.5+dfsg/dialign' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/dialign' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/dialign' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/dialign' Making install in Align make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Align' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Align' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Align' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Align' Making install in ABYSS make[3]: Entering directory '/build/abyss-2.3.5+dfsg/ABYSS' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/ABYSS' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c ABYSS '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/ABYSS' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Parallel' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Parallel' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Parallel' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Parallel' Making install in Bloom make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Bloom' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Bloom' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-bloom '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Bloom' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/abyss-2.3.5+dfsg/BloomDBG' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/BloomDBG' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-bloom-dbg '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/BloomDBG' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Konnector' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Konnector' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c konnector '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Konnector' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Consensus' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Consensus' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Consensus '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Consensus' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-2.3.5+dfsg/DAssembler' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DAssembler' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c DAssembler '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DAssembler' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/abyss-2.3.5+dfsg/DistanceEst' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/DistanceEst' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/DistanceEst' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/abyss-2.3.5+dfsg/KAligner' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/KAligner' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c KAligner '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/KAligner' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/KAligner' Making install in Layout make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Layout' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Layout' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-layout '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Layout' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-2.3.5+dfsg/LogKmerCount' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/LogKmerCount' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c logcounter '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/LogKmerCount' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Map' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Map' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Map' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Map' Making install in MergePaths make[3]: Entering directory '/build/abyss-2.3.5+dfsg/MergePaths' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/MergePaths' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/MergePaths' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/MergePaths' Making install in Overlap make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Overlap' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Overlap' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Overlap '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Overlap' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/abyss-2.3.5+dfsg/PairedDBG' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PairedDBG' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-2.3.5+dfsg/ParseAligns' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/ParseAligns' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-2.3.5+dfsg/PathOverlap' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PathOverlap' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-2.3.5+dfsg/PopBubbles' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/PopBubbles' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c PopBubbles '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/PopBubbles' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Scaffold' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Scaffold' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Scaffold' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/abyss-2.3.5+dfsg/SimpleGraph' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/SimpleGraph' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/abyss-2.3.5+dfsg/kmerprint' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/kmerprint' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/kmerprint' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/abyss-2.3.5+dfsg/FilterGraph' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/FilterGraph' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-filtergraph '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/FilterGraph' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/abyss-2.3.5+dfsg/GapFiller' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/GapFiller' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-gapfill '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/GapFiller' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/GapFiller' Making install in Sealer make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Sealer' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Sealer' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Sealer' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Sealer' Making install in RResolver make[3]: Entering directory '/build/abyss-2.3.5+dfsg/RResolver' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/RResolver' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-rresolver-short '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/RResolver' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/RResolver' Making install in AdjList make[3]: Entering directory '/build/abyss-2.3.5+dfsg/AdjList' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/AdjList' /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c AdjList '/build/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/AdjList' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/AdjList' Making install in vendor make[3]: Entering directory '/build/abyss-2.3.5+dfsg/vendor' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/vendor' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/vendor' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/vendor' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/abyss-2.3.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-2.3.5+dfsg/Unittest' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.3.5+dfsg/Unittest' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg/Unittest' make[3]: Entering directory '/build/abyss-2.3.5+dfsg' make[4]: Entering directory '/build/abyss-2.3.5+dfsg' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-2.3.5+dfsg' make[3]: Leaving directory '/build/abyss-2.3.5+dfsg' make[2]: Leaving directory '/build/abyss-2.3.5+dfsg' mkdir -p debian/tmp/usr/share/man/man1 PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path 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/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path help2man --no-info \ -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \ > debian/tmp/usr/share/man/man1/abyss-fixmate.1 make[1]: Leaving directory '/build/abyss-2.3.5+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/abyss-2.3.5+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/abyss-2.3.5+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.5+dfsg-2_amd64.deb'. dpkg-deb: building package 'abyss' in '../abyss_2.3.5+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../abyss_2.3.5+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../abyss_2.3.5+dfsg-2_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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1880974/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1880974/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1880974 and its subdirectories I: Current time: Fri May 5 19:55:25 +14 2023 I: pbuilder-time-stamp: 1683266125