I: pbuilder: network access will be disabled during build I: Current time: Tue Aug 1 05:21:40 -12 2023 I: pbuilder-time-stamp: 1690910500 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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_2.2.5+dfsg-1.dsc] I: copying [./abyss_2.2.5+dfsg.orig.tar.xz] I: copying [./abyss_2.2.5+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.0K3otDcA/trustedkeys.kbx': General error gpgv: Signature made Fri Dec 4 01:53:32 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./abyss_2.2.5+dfsg-1.dsc dpkg-source: info: extracting abyss in abyss-2.2.5+dfsg dpkg-source: info: unpacking abyss_2.2.5+dfsg.orig.tar.xz dpkg-source: info: unpacking abyss_2.2.5+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3835407/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='2205404479f44e37a9e09d2e1925017f' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3835407' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.9ihDLiJw/pbuilderrc_zXwS --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9ihDLiJw/b1 --logfile b1/build.log abyss_2.2.5+dfsg-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 6 21:25 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/3835407/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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19707 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. 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-10{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{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-10-dev{a} libgfortran5{a} libglib2.0-0{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} libicu67{a} libjs-jquery{a} libjs-jquery-ui{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmd0{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} libpmix-dev{a} libpmix2{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} libsigsegv2{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} 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 libglib2.0-data libhttp-message-perl libmail-sendmail-perl lynx shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 106 newly installed, 0 to remove and 0 not upgraded. Need to get 68.5 MB of archives. After unpacking 389 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libcbor0 amd64 0.5.0+dfsg-2 [24.0 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libfido2-1 amd64 1.6.0-2 [53.3 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 openssh-client amd64 1:8.4p1-5+deb11u1 [929 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libgfortran-10-dev amd64 10.2.1-6 [769 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 gfortran-10 amd64 10.2.1-6 [9447 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libibverbs1 amd64 33.2-1 [59.4 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 ibverbs-providers amd64 33.2-1 [253 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 icu-devtools amd64 67.1-7 [201 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74.0 amd64 1.74.0-9 [516 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libboost-graph1.74.0 amd64 1.74.0-9 [326 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libicu-dev amd64 67.1-7 [9597 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74-dev amd64 1.74.0-9 [588 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libboost-serialization1.74.0 amd64 1.74.0-9 [340 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libboost-serialization1.74-dev amd64 1.74.0-9 [383 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libboost-test1.74.0 amd64 1.74.0-9 [472 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libboost-test1.74-dev amd64 1.74.0-9 [547 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libboost-graph1.74-dev amd64 1.74.0-9 [346 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libboost-graph-dev amd64 1.74.0.3 [4436 B] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libevent-2.1-7 amd64 2.1.12-stable-1 [188 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [139 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-1 [110 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [57.1 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-1 [64.1 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libevent-dev amd64 2.1.12-stable-1 [311 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.1 [169 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libnuma1 amd64 2.0.12-1+b1 [26.3 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libpsm2-2 amd64 11.2.185-1 [181 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 librdmacm1 amd64 33.2-1 [68.9 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libfabric1 amd64 1.11.0-2 [521 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 liburi-perl all 5.08-1 [90.6 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libhtml-parser-perl amd64 3.75-1+b1 [105 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libhwloc15 amd64 2.4.1+dfsg-1 [150 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libnuma-dev amd64 2.0.12-1+b1 [39.3 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libltdl7 amd64 2.4.6-15 [391 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libltdl-dev amd64 2.4.6-15 [162 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libhwloc-dev amd64 2.4.1+dfsg-1 [231 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libxnvctrl0 amd64 470.141.03-1~deb11u1 [27.5 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 ocl-icd-libopencl1 amd64 2.2.14-2 [42.5 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libhwloc-plugins amd64 2.4.1+dfsg-1 [21.4 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libnl-3-dev amd64 3.4.0-1+b1 [102 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libnl-route-3-dev amd64 3.4.0-1+b1 [176 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libibverbs-dev amd64 33.2-1 [487 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libpmix2 amd64 4.0.0-4.1 [552 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libucx0 amd64 1.10.1~rc1+really.1.10.0-1 [649 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libopenmpi3 amd64 4.1.0-10 [2370 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 openmpi-common all 4.1.0-10 [179 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libpmix-dev amd64 4.0.0-4.1 [655 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 openmpi-bin amd64 4.1.0-10 [238 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libopenmpi-dev amd64 4.1.0-10 [1192 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-dev amd64 3.34.1-3 [963 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libtext-markdown-perl all 1.000031-3 [33.8 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libtext-multimarkdown-perl all 1.000035-2 [28.6 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Fetched 68.5 MB in 3s (21.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19707 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../001-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. 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Preparing to unpack .../065-libnuma1_2.0.12-1+b1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.12-1+b1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../066-libpsm2-2_11.2.185-1_amd64.deb ... Unpacking libpsm2-2 (11.2.185-1) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../067-librdmacm1_33.2-1_amd64.deb ... Unpacking librdmacm1:amd64 (33.2-1) ... Selecting previously unselected package libfabric1. Preparing to unpack .../068-libfabric1_1.11.0-2_amd64.deb ... Unpacking libfabric1 (1.11.0-2) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../069-libglib2.0-0_2.66.8-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.66.8-1) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../070-libhtml-tagset-perl_3.20-4_all.deb ... Unpacking libhtml-tagset-perl (3.20-4) ... Selecting previously unselected package liburi-perl. 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Preparing to unpack .../077-libhwloc-dev_2.4.1+dfsg-1_amd64.deb ... Unpacking libhwloc-dev:amd64 (2.4.1+dfsg-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../078-libpciaccess0_0.16-1_amd64.deb ... Unpacking libpciaccess0:amd64 (0.16-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../079-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 .../080-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 .../081-libxcb1_1.14-3_amd64.deb ... Unpacking libxcb1:amd64 (1.14-3) ... Selecting previously unselected package libx11-data. Preparing to unpack .../082-libx11-data_2%3a1.7.2-1_all.deb ... Unpacking libx11-data (2:1.7.2-1) ... Selecting previously unselected package libx11-6:amd64. 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Preparing to unpack .../105-pkg-config_0.29.2-1_amd64.deb ... Unpacking pkg-config (0.29.2-1) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up libtext-markdown-perl (1.000031-3) ... Setting up libpciaccess0:amd64 (0.16-1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libboost1.74-dev:amd64 (1.74.0-9) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.66.8-1) ... No schema files found: doing nothing. Setting up libhtml-tagset-perl (3.20-4) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libcbor0:amd64 (0.5.0+dfsg-2) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libboost-test1.74.0:amd64 (1.74.0-9) ... Setting up libsqlite3-dev:amd64 (3.34.1-3) ... Setting up libx11-data (2:1.7.2-1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libboost-regex1.74.0:amd64 (1.74.0-9) ... Setting up libhwloc15:amd64 (2.4.1+dfsg-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libevent-2.1-7:amd64 (2.1.12-stable-1) ... Setting up libboost-graph1.74.0:amd64 (1.74.0-9) ... Setting up autopoint (0.21-4) ... Setting up icu-devtools (67.1-7) ... Setting up pkg-config (0.29.2-1) ... Setting up libltdl7:amd64 (2.4.6-15) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libboost-serialization1.74.0:amd64 (1.74.0-9) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libnuma1:amd64 (2.0.12-1+b1) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up ocl-icd-libopencl1:amd64 (2.2.14-2) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libnl-3-200:amd64 (3.4.0-1+b1) ... Setting up libpsm2-2 (11.2.185-1) ... Setting up openmpi-common (4.1.0-10) ... Setting up libsub-override-perl (0.09-2) ... Setting up libgfortran-10-dev:amd64 (10.2.1-6) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ... 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 (3.5.1+dfsg+~3.5.5-7) ... Setting up libfido2-1:amd64 (1.6.0-2) ... Setting up libboost-test1.74-dev:amd64 (1.74.0-9) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libicu-dev:amd64 (67.1-7) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up liburi-perl (5.08-1) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-1) ... 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Setting up libnl-3-dev:amd64 (3.4.0-1+b1) ... Setting up groff-base (1.22.4-6) ... Setting up libhtml-parser-perl (3.75-1+b1) ... Setting up libx11-6:amd64 (2:1.7.2-1) ... Setting up libtext-multimarkdown-perl (1.000035-2) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libibverbs1:amd64 (33.2-1) ... Setting up ibverbs-providers:amd64 (33.2-1) ... Setting up openssh-client (1:8.4p1-5+deb11u1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:amd64 (470.141.03-1~deb11u1) ... Setting up dh-autoreconf (20) ... Setting up libnl-route-3-dev:amd64 (3.4.0-1+b1) ... Setting up libltdl-dev:amd64 (2.4.6-15) ... Setting up libboost-graph1.74-dev:amd64 (1.74.0-9) ... Setting up libhwloc-dev:amd64 (2.4.1+dfsg-1) ... Setting up librdmacm1:amd64 (33.2-1) ... Setting up libboost-graph-dev:amd64 (1.74.0.3) ... Setting up libucx0:amd64 (1.10.1~rc1+really.1.10.0-1) ... Setting up debhelper (13.3.4) ... Setting up libibverbs-dev:amd64 (33.2-1) ... Setting up libhwloc-plugins:amd64 (2.4.1+dfsg-1) ... Setting up libfabric1 (1.11.0-2) ... Setting up libpmix2:amd64 (4.0.0-4.1) ... Setting up libopenmpi3:amd64 (4.1.0-10) ... Setting up libpmix-dev:amd64 (4.0.0-4.1) ... Setting up openmpi-bin (4.1.0-10) ... 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 (4.1.0-10) ... 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 (2.31-13+deb11u6) ... 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 I: Building the package I: Running cd /build/abyss-2.2.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../abyss_2.2.5+dfsg-1_source.changes dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.2.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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:167: installing './config.guess' configure.ac:167: 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-2.2.5+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 we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes 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 thread-safe mkdir -p... /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 dependency style of g++ -std=c++11... none checking for gawk... (cached) mawk checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 we are using the GNU C++ compiler... (cached) yes checking whether g++ -std=c++11 accepts -g... (cached) yes checking for ranlib... ranlib checking for ghc... no ./configure: line 5926: : command not found checking for pandoc... no checking for ar... ar checking the archiver (ar) interface... ar checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for ANSI C header files... (cached) 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 vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... 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 mpi.h usability... yes checking mpi.h presence... 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 how to run the C++ preprocessor... g++ -std=c++11 -E checking functional usability... yes checking functional presence... yes checking for functional... yes checking tr1/functional usability... yes checking tr1/functional presence... yes checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes checking boost/property_map/property_map.hpp usability... yes checking boost/property_map/property_map.hpp presence... yes checking for boost/property_map/property_map.hpp... yes checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes checking unordered_map usability... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking boost/unordered_set.hpp usability... yes checking boost/unordered_set.hpp presence... yes checking for boost/unordered_set.hpp... yes checking sqlite3.h usability... yes checking sqlite3.h presence... 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 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-2.2.5+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-2.2.5+dfsg' dh_auto_build make -j15 make[2]: Entering directory '/build/abyss-2.2.5+dfsg' make all-recursive make[3]: Entering directory '/build/abyss-2.2.5+dfsg' Making all in bin make[4]: Entering directory '/build/abyss-2.2.5+dfsg/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/bin' Making all in doc make[4]: Entering directory '/build/abyss-2.2.5+dfsg/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/doc' Making all in Common make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Common' Making all in Graph make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Graph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Graph' Making all in DataLayer make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-2.2.5+dfsg/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/FMIndex' Making all in Assembly make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Assembly' Making all in dialign make[4]: Entering directory '/build/abyss-2.2.5+dfsg/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function 'calc_weight' declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ assemble.c:40:20: warning: inline function 'align_diag' declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ io.c: In function 'read_scr_matrix': io.c:270:3: 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': 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, | ^~~~~~~~~~~ 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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diag.c:1456:3: 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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/dialign' Making all in Align make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Align' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Align' Making all in ABYSS make[4]: Entering directory '/build/abyss-2.2.5+dfsg/ABYSS' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/ABYSS' Making all in Parallel make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Parallel' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Parallel' Making all in Bloom make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Bloom' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/abyss-2.2.5+dfsg/BloomDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Konnector' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Konnector' Making all in Consensus make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Consensus' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Consensus' Making all in DAssembler make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DAssembler' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DistanceEst' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-2.2.5+dfsg/KAligner' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/KAligner' Making all in Layout make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Layout' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/abyss-2.2.5+dfsg/LogKmerCount' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/LogKmerCount' Making all in Map make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Map' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Map' Making all in MergePaths make[4]: Entering directory '/build/abyss-2.2.5+dfsg/MergePaths' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/MergePaths' Making all in Overlap make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Overlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/abyss-2.2.5+dfsg/PairedDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/abyss-2.2.5+dfsg/ParseAligns' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-2.2.5+dfsg/PathOverlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/abyss-2.2.5+dfsg/PopBubbles' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Scaffold' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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 -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/abyss-2.2.5+dfsg/SimpleGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/abyss-2.2.5+dfsg/kmerprint' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/abyss-2.2.5+dfsg/FilterGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/GapFiller' Making all in Sealer make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Sealer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Sealer' Making all in AdjList make[4]: Entering directory '/build/abyss-2.2.5+dfsg/AdjList' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/AdjList' Making all in vendor make[4]: Entering directory '/build/abyss-2.2.5+dfsg/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/vendor' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/build/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-2.2.5+dfsg' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg' make[2]: Leaving directory '/build/abyss-2.2.5+dfsg' markdown README.md > README.html make[1]: Leaving directory '/build/abyss-2.2.5+dfsg' dh_auto_test make -j15 check VERBOSE=1 make[1]: Entering directory '/build/abyss-2.2.5+dfsg' Making check in bin make[2]: Entering directory '/build/abyss-2.2.5+dfsg/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/bin' Making check in doc make[2]: Entering directory '/build/abyss-2.2.5+dfsg/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/doc' Making check in Common make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Common' Making check in Graph make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Graph' Making check in DataLayer make[2]: Entering directory '/build/abyss-2.2.5+dfsg/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/DataLayer' Making check in DataBase make[2]: Entering directory '/build/abyss-2.2.5+dfsg/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/DataBase' Making check in FMIndex make[2]: Entering directory '/build/abyss-2.2.5+dfsg/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/FMIndex' Making check in Assembly make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Assembly' Making check in dialign make[2]: Entering directory '/build/abyss-2.2.5+dfsg/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/dialign' Making check in Align make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Align' Making check in ABYSS make[2]: Entering directory '/build/abyss-2.2.5+dfsg/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/ABYSS' Making check in Parallel make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Parallel' Making check in Bloom make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Bloom' Making check in BloomDBG make[2]: Entering directory '/build/abyss-2.2.5+dfsg/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/BloomDBG' Making check in Konnector make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Konnector' Making check in Consensus make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Consensus' Making check in DAssembler make[2]: Entering directory '/build/abyss-2.2.5+dfsg/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/abyss-2.2.5+dfsg/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/abyss-2.2.5+dfsg/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/KAligner' Making check in Layout make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/abyss-2.2.5+dfsg/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/LogKmerCount' Making check in Map make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Map' Making check in MergePaths make[2]: Entering directory '/build/abyss-2.2.5+dfsg/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/MergePaths' Making check in Overlap make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Overlap' Making check in PairedDBG make[2]: Entering directory '/build/abyss-2.2.5+dfsg/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/build/abyss-2.2.5+dfsg/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/abyss-2.2.5+dfsg/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/abyss-2.2.5+dfsg/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/abyss-2.2.5+dfsg/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/abyss-2.2.5+dfsg/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/abyss-2.2.5+dfsg/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/abyss-2.2.5+dfsg/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/GapFiller' Making check in Sealer make[2]: Entering directory '/build/abyss-2.2.5+dfsg/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Sealer' Making check in AdjList make[2]: Entering directory '/build/abyss-2.2.5+dfsg/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/AdjList' Making check in vendor make[2]: Entering directory '/build/abyss-2.2.5+dfsg/vendor' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/vendor' Making check in vendor/gtest-1.7.0 make[2]: Entering directory '/build/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/vendor/gtest-1.7.0' make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/abyss-2.2.5+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-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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 -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-2.2.5+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-2.2.5+dfsg/Unittest' make check-TESTS make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Unittest' PASS: common_stringutil PASS: common_bitutil PASS: common_histogram PASS: common_kmer PASS: common_sequence PASS: common_KmerIterator PASS: BloomFilter PASS: common_sam PASS: Konnector_DBGBloom PASS: common_sam_ssq PASS: Konnector_DBGBloomAlgorithms PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ExtendPath PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_DotIO PASS: graph_UndirectedGraph PASS: Konnector_konnector PASS: PairedDBG_Dinuc PASS: PairedDBG_KmerPair PASS: PairedDBG_BranchRecord PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_SpacedSeed PASS: BloomDBG_MaskedKmer PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_LightweightKmer PASS: PairedDBG_LoadAlgorithm PASS: DBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.2.5 ============================================================================ # TOTAL: 34 # PASS: 34 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Unittest' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Unittest' make[2]: Leaving directory '/build/abyss-2.2.5+dfsg/Unittest' make[2]: Entering directory '/build/abyss-2.2.5+dfsg' make[2]: Leaving directory '/build/abyss-2.2.5+dfsg' make[1]: Leaving directory '/build/abyss-2.2.5+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-2.2.5+dfsg' dh_auto_install --destdir=debian/tmp make -j15 install DESTDIR=/build/abyss-2.2.5\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-2.2.5+dfsg' Making install in bin make[3]: Entering directory '/build/abyss-2.2.5+dfsg/bin' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/bin' /bin/mkdir -p '/build/abyss-2.2.5+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-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/bin' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/bin' Making install in doc make[3]: Entering directory '/build/abyss-2.2.5+dfsg/doc' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/doc' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/doc' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/doc' Making install in Common make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Common' make[4]: Entering directory '/build/abyss-2.2.5+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-2.2.5+dfsg/Common' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Common' Making install in Graph make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Graph' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Graph' /bin/mkdir -p '/build/abyss-2.2.5+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-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Graph' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Graph' Making install in DataLayer make[3]: Entering directory '/build/abyss-2.2.5+dfsg/DataLayer' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DataLayer' /bin/mkdir -p '/build/abyss-2.2.5+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-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DataLayer' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/DataLayer' Making install in DataBase make[3]: Entering directory '/build/abyss-2.2.5+dfsg/DataBase' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DataBase' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-db-txt '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DataBase' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/DataBase' Making install in FMIndex make[3]: Entering directory '/build/abyss-2.2.5+dfsg/FMIndex' make[4]: Entering directory '/build/abyss-2.2.5+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-2.2.5+dfsg/FMIndex' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/FMIndex' Making install in Assembly make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Assembly' make[4]: Entering directory '/build/abyss-2.2.5+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-2.2.5+dfsg/Assembly' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Assembly' Making install in dialign make[3]: Entering directory '/build/abyss-2.2.5+dfsg/dialign' make[4]: Entering directory '/build/abyss-2.2.5+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-2.2.5+dfsg/dialign' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/dialign' Making install in Align make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Align' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Align' /bin/mkdir -p '/build/abyss-2.2.5+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-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Align' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Align' Making install in ABYSS make[3]: Entering directory '/build/abyss-2.2.5+dfsg/ABYSS' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/ABYSS' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c ABYSS '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/ABYSS' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Parallel' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Parallel' /bin/mkdir -p '/build/abyss-2.2.5+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-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Parallel' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Parallel' Making install in Bloom make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Bloom' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Bloom' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Bloom' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/abyss-2.2.5+dfsg/BloomDBG' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/BloomDBG' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-bloom-dbg '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/BloomDBG' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Konnector' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Konnector' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c konnector '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Konnector' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Consensus' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Consensus' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Consensus '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Consensus' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-2.2.5+dfsg/DAssembler' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DAssembler' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c DAssembler '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DAssembler' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/abyss-2.2.5+dfsg/DistanceEst' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/DistanceEst' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/abyss-2.2.5+dfsg/KAligner' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/KAligner' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c KAligner '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/KAligner' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/KAligner' Making install in Layout make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Layout' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Layout' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-layout '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Layout' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-2.2.5+dfsg/LogKmerCount' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/LogKmerCount' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c logcounter '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/LogKmerCount' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Map' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Map' /bin/mkdir -p '/build/abyss-2.2.5+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-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Map' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Map' Making install in MergePaths make[3]: Entering directory '/build/abyss-2.2.5+dfsg/MergePaths' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/MergePaths' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/MergePaths' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/MergePaths' Making install in Overlap make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Overlap' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Overlap' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Overlap '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Overlap' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/abyss-2.2.5+dfsg/PairedDBG' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/PairedDBG' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-paired-dbg '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/PairedDBG' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-2.2.5+dfsg/ParseAligns' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/ParseAligns' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-2.2.5+dfsg/PathOverlap' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/PathOverlap' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c PathOverlap '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/PathOverlap' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-2.2.5+dfsg/PopBubbles' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/PopBubbles' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c PopBubbles '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/PopBubbles' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Scaffold' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Scaffold' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/abyss-2.2.5+dfsg/SimpleGraph' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/SimpleGraph' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c SimpleGraph '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/SimpleGraph' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/abyss-2.2.5+dfsg/kmerprint' make[4]: Entering directory '/build/abyss-2.2.5+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-2.2.5+dfsg/kmerprint' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/abyss-2.2.5+dfsg/FilterGraph' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/FilterGraph' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-filtergraph '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/FilterGraph' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/abyss-2.2.5+dfsg/GapFiller' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/GapFiller' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-gapfill '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/GapFiller' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/GapFiller' Making install in Sealer make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Sealer' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/Sealer' /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/Sealer' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Sealer' Making install in AdjList make[3]: Entering directory '/build/abyss-2.2.5+dfsg/AdjList' make[4]: Entering directory '/build/abyss-2.2.5+dfsg/AdjList' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg/AdjList' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/AdjList' Making install in vendor make[3]: Entering directory '/build/abyss-2.2.5+dfsg/vendor' make[4]: Entering directory '/build/abyss-2.2.5+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-2.2.5+dfsg/vendor' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/vendor' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/build/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' make[4]: Entering directory '/build/abyss-2.2.5+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-2.2.5+dfsg/vendor/gtest-1.7.0' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/abyss-2.2.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-2.2.5+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-2.2.5+dfsg/Unittest' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg/Unittest' make[3]: Entering directory '/build/abyss-2.2.5+dfsg' make[4]: Entering directory '/build/abyss-2.2.5+dfsg' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-2.2.5+dfsg' make[3]: Leaving directory '/build/abyss-2.2.5+dfsg' make[2]: Leaving directory '/build/abyss-2.2.5+dfsg' PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ -n "Estimate distances between contigs using paired-end alignments." \ DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1 PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \ -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \ > debian/tmp/usr/share/man/man1/abyss-fixmate.1 make[1]: Leaving directory '/build/abyss-2.2.5+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/abyss-2.2.5+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-2.2.5+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' in '../abyss_2.2.5+dfsg-1_amd64.deb'. dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.2.5+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../abyss_2.2.5+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration 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/3835407 and its subdirectories I: Current time: Tue Aug 1 05:45:40 -12 2023 I: pbuilder-time-stamp: 1690911940