Mon Nov 29 07:44:49 UTC 2021 I: starting to build abyss/buster/amd64 on jenkins on '2021-11-29 07:44' Mon Nov 29 07:44:49 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_16/90847/console.log Mon Nov 29 07:44:49 UTC 2021 I: Downloading source for buster/abyss=2.1.5-7 --2021-11-29 07:44:49-- http://deb.debian.org/debian/pool/main/a/abyss/abyss_2.1.5-7.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2356 (2.3K) Saving to: ‘abyss_2.1.5-7.dsc’ 0K .. 100% 9.08M=0s 2021-11-29 07:44:49 (9.08 MB/s) - ‘abyss_2.1.5-7.dsc’ saved [2356/2356] Mon Nov 29 07:44:49 UTC 2021 I: abyss_2.1.5-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: abyss Binary: abyss Architecture: any-amd64 any-i386 arm64 armel armhf mips64el mipsel ppc64el s390x alpha ia64 m68k powerpcspe ppc64 riscv64 sh4 sparc64 Version: 2.1.5-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/abyss Vcs-Git: https://salsa.debian.org/med-team/abyss.git Testsuite: autopkgtest Build-Depends: debhelper (>= 12~), python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, libsqlite3-dev, pkg-config, help2man Package-List: abyss deb science optional arch=any-amd64,arm64,armel,armhf,any-i386,mips64el,mipsel,ppc64el,s390x,alpha,ia64,m68k,powerpcspe,ppc64,riscv64,sh4,sparc64,x32 Checksums-Sha1: a513525e2249705f20bddfc3a0bdacb61a8ccd13 1063069 abyss_2.1.5.orig.tar.gz 8e94fff11446478468f2e7c4131fbe18284a38ee 760232 abyss_2.1.5-7.debian.tar.xz Checksums-Sha256: cfd6091fa4b762e44e7427a9a710737614d73161b51309952ace202d6d904b50 1063069 abyss_2.1.5.orig.tar.gz ccbd386f28daced0cc209da27c2b35a926a4fed4cff67bdce60b269b8fbfcdef 760232 abyss_2.1.5-7.debian.tar.xz Files: a716fc1ca89597283e2a5866ac78ff06 1063069 abyss_2.1.5.orig.tar.gz b06b7a0f4e6f33653881a14e0dd64329 760232 abyss_2.1.5-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAlxpX5wACgkQPCZ2P2xn 5uJQdxAAuZTIvCTCrW9Fhu9AlXqU3N/vN2CMdIiMDnANLGz4H0fZ3jEG1hMg0gLB +B55gIpvnHTfxMjSCkm1sZFyFNPHcp99MHCE8JEOM7EPIgrC/SjC7rLdMAghKlg0 AWrdDWdvDqhBHdoHspYS3wqGWmbZMFoX0x8X8xI6VCo0ywTe2yH5E2pDaQ8vPUi5 qCH5qaCEm/A3D3I4hXY5xlR9Zy/OvBBhWm5hF1jzZCfx5eDNU86ElH+4D47VCQju eq0HmJUYjWecceEgF0NUMrKHhD6rGj+UNNTxmHdS8xQ6cDZm6/X2m4EfDIDz4r7E IAaA85rfEsxfOqdV0qcsbwCq+e+gm6U4x7y2+I4b+ovg531C+zwzKJ1pAXS/ssX2 PCkl3bFZLGN5n/WJ9y7aSWlxWN7/BqN0DMUw8HJQBmXKtMyxITYYgSULvwPDV8UW L2EifIcQuOqO9okNL7SKhloD6F6uVIApArs9HdiN0BWHkXmovMDf8CElIusHPnmN 0C+pSVeY8w8FXvz3O4L49nWnX04T22vC6b/HXQryBnVMj57QxAofe6RztlQGnRv/ obFky7h6drd/Pww9jliLyF8JDNgVtAIipW1F+XufWEWW12ecGFRGdWibqhzxlTKr eYzD8qnU9aKRUixyauqSdnH3o/jyOAo+ryKNNc4sIF/s8UCWtjM= =FF9C -----END PGP SIGNATURE----- Mon Nov 29 07:44:49 UTC 2021 I: Checking whether the package is not for us Mon Nov 29 07:44:49 UTC 2021 I: Starting 1st build on remote node ionos15-amd64.debian.net. Mon Nov 29 07:44:49 UTC 2021 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Mon Nov 29 07:51:29 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 1 02:07:54 -12 2023 I: pbuilder-time-stamp: 1672582074 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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_2.1.5-7.dsc] I: copying [./abyss_2.1.5.orig.tar.gz] I: copying [./abyss_2.1.5-7.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Feb 17 01:20:28 2019 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./abyss_2.1.5-7.dsc dpkg-source: info: extracting abyss in abyss-2.1.5 dpkg-source: info: unpacking abyss_2.1.5.orig.tar.gz dpkg-source: info: unpacking abyss_2.1.5-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying abyss-32-bit.patch dpkg-source: info: applying fix_bash_script.patch dpkg-source: info: applying big_endian.patch dpkg-source: info: applying strict_alignment.patch dpkg-source: info: applying hurd.patch dpkg-source: info: applying fix_implicit-function-declaration dpkg-source: info: applying spelling I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2150296/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 parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='94fc609b61dd47dfa1f7e08570613c6c' 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='2150296' 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/tmp.7CccSBudTb/pbuilderrc_H5oo --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.7CccSBudTb/b1 --logfile b1/build.log abyss_2.1.5-7.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://85.184.249.68:3128' I: uname -a Linux ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Dec 10 16:20 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/2150296/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 (>= 12~), python-markdown, libboost-graph-dev, libopenmpi-dev, libsparsehash-dev, libtext-multimarkdown-perl, libgtest-dev, 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 ... 19195 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 (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on python-markdown; however: Package python-markdown 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 libgtest-dev; however: Package libgtest-dev 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} help2man{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libboost-chrono1.67.0{a} libboost-graph-dev{a} libboost-graph1.67-dev{a} libboost-graph1.67.0{a} libboost-regex1.67.0{a} libboost-serialization1.67-dev{a} libboost-serialization1.67.0{a} libboost-test1.67-dev{a} libboost-test1.67.0{a} libboost-timer1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libedit2{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libexpat1{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libgtest-dev{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{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} libpmix2{a} libpsm-infinipath1{a} libpsm2-2{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} librdmacm1{a} libreadline7{a} libsigsegv2{a} libsparsehash-dev{a} libsqlite3-dev{a} libssl1.1{a} libtext-markdown-perl{a} libtext-multimarkdown-perl{a} libtool{a} libuchardet0{a} liburi-perl{a} libxml2{a} m4{a} man-db{a} mime-support{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} po-debconf{a} python{a} python-markdown{a} python-minimal{a} python-pkg-resources{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libhttp-message-perl libmail-sendmail-perl lynx python-pygments python-yaml shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 109 newly installed, 0 to remove and 0 not upgraded. Need to get 49.0 MB of archives. After unpacking 302 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 openssh-client amd64 1:7.9p1-10+deb10u2 [782 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 googletest amd64 1.8.1-3 [903 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libnl-3-200 amd64 3.4.0-1 [63.0 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libnl-route-3-200 amd64 3.4.0-1 [162 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libibverbs1 amd64 22.1-1 [51.2 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 ibverbs-providers amd64 22.1-1 [187 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 libboost-chrono1.67.0 amd64 1.67.0-13+deb10u1 [234 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67.0 amd64 1.67.0-13+deb10u1 [485 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libboost-graph1.67.0 amd64 1.67.0-13+deb10u1 [316 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libboost-serialization1.67.0 amd64 1.67.0-13+deb10u1 [319 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 libboost-serialization1.67-dev amd64 1.67.0-13+deb10u1 [359 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libboost-timer1.67.0 amd64 1.67.0-13+deb10u1 [231 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libboost-test1.67.0 amd64 1.67.0-13+deb10u1 [456 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libboost-test1.67-dev amd64 1.67.0-13+deb10u1 [511 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libboost-graph1.67-dev amd64 1.67.0-13+deb10u1 [325 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libboost-graph-dev amd64 1.67.0.1 [3752 B] Get: 74 http://deb.debian.org/debian buster/main amd64 libevent-2.1-6 amd64 2.1.8-stable-4 [177 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4 [129 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 libevent-pthreads-2.1-6 amd64 2.1.8-stable-4 [47.9 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6 [168 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libpsm2-2 amd64 11.2.78-1 [177 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 librdmacm1 amd64 22.1-1 [65.3 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libfabric1 amd64 1.6.2-3 [396 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libgtest-dev amd64 1.8.1-3 [223 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 libltdl7 amd64 2.4.6-9 [390 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libhwloc5 amd64 1.11.12-3 [111 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libnuma-dev amd64 2.0.12-1 [39.2 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libltdl-dev amd64 2.4.6-9 [162 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libhwloc-dev amd64 1.11.12-3 [175 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 ocl-icd-libopencl1 amd64 2.2.12-2 [37.5 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 libhwloc-plugins amd64 1.11.12-3 [17.4 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 libnl-3-dev amd64 3.4.0-1 [102 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libnl-route-3-dev amd64 3.4.0-1 [177 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libibverbs-dev amd64 22.1-1 [362 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libpmix2 amd64 3.1.2-3 [498 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 libopenmpi3 amd64 3.1.3-11 [2191 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 openmpi-common all 3.1.3-11 [165 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 openmpi-bin amd64 3.1.3-11 [200 kB] Get: 102 http://deb.debian.org/debian buster/main amd64 libopenmpi-dev amd64 3.1.3-11 [974 kB] Get: 103 http://deb.debian.org/debian buster/main amd64 libsparsehash-dev all 2.0.2-1 [76.9 kB] Get: 104 http://deb.debian.org/debian buster/main amd64 libsqlite3-dev amd64 3.27.2-3+deb10u1 [787 kB] Get: 105 http://deb.debian.org/debian buster/main amd64 libtext-markdown-perl all 1.000031-2 [34.4 kB] Get: 106 http://deb.debian.org/debian buster/main amd64 libtext-multimarkdown-perl all 1.000035-1 [29.4 kB] Get: 107 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] Get: 108 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 109 http://deb.debian.org/debian buster/main amd64 python-markdown all 3.0.1-3 [60.6 kB] Fetched 49.0 MB in 1s (81.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../14-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:amd64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_amd64.deb ... Unpacking libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_amd64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:amd64. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython2-stdlib:amd64 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.16-1) ... Setting up libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20658 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_amd64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20691 files and directories currently installed.) Preparing to unpack .../00-python_2.7.16-1_amd64.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../04-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../07-libedit2_3.1-20181209-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20181209-1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../08-libkeyutils1_1.6-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6-6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../09-libkrb5support0_1.17-3+deb10u3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../10-libk5crypto3_1.17-3+deb10u3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../11-libkrb5-3_1.17-3+deb10u3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../12-libgssapi-krb5-2_1.17-3+deb10u3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Selecting previously unselected package openssh-client. Preparing to unpack .../13-openssh-client_1%3a7.9p1-10+deb10u2_amd64.deb ... Unpacking openssh-client (1:7.9p1-10+deb10u2) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../14-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../15-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../16-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../17-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../18-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../19-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../20-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../21-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../22-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../23-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../24-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../25-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../26-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../27-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../28-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../29-libxml2_2.9.4+dfsg1-7+deb10u2_amd64.deb ... Unpacking libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../30-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../31-libncurses6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. 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Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up libnl-3-dev:amd64 (3.4.0-1) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up libboost-graph1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libtext-multimarkdown-perl (1.000035-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libboost-graph-dev:amd64 (1.67.0.1) ... Setting up libibverbs1:amd64 (22.1-1) ... Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpmix2:amd64 (3.1.2-3) ... 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Setting up openmpi-bin (3.1.3-11) ... 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 (3.1.3-11) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/abyss-2.1.5/ && 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_2.1.5-7_source.changes dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.1.5-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf configure.ac:11: installing './compile' configure.ac:161: installing './config.guess' configure.ac:161: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/abyss-2.1.5' 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-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 configure: WARNING: unrecognized options: --disable-maintainer-mode 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 nested variables... yes checking for gawk... 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(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++ -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++ 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 Misc/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 lib/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 lib/bloomfilter/Makefile config.status: creating lib/nthash/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/abyss-2.1.5' debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-2.1.5' dh_auto_build make -j16 make[2]: Entering directory '/build/abyss-2.1.5' make all-recursive make[3]: Entering directory '/build/abyss-2.1.5' Making all in bin make[4]: Entering directory '/build/abyss-2.1.5/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/bin' Making all in doc make[4]: Entering directory '/build/abyss-2.1.5/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/doc' Making all in Common make[4]: Entering directory '/build/abyss-2.1.5/Common' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Common' Making all in Graph make[4]: Entering directory '/build/abyss-2.1.5/Graph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Graph' Making all in DataLayer make[4]: Entering directory '/build/abyss-2.1.5/DataLayer' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.1.5/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-2.1.5/DataBase' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-2.1.5/FMIndex' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/FMIndex' Making all in Assembly make[4]: Entering directory '/build/abyss-2.1.5/Assembly' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Assembly' Making all in dialign make[4]: Entering directory '/build/abyss-2.1.5/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c diag.c:1456:3: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); ^~~~~~~~~~~~~~~~ alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined 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 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 extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); ^~~~~~~~~~ assemble.c:37:32: warning: inline function 'find_eqc' declared but never defined 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 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 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 extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, ^~~~~~~~~~~ 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] fscanf( fp, "%i", &is); ^~~~~~~~~~~~~~~~~~~~~~ io.c:282:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%s\n", rline); ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'read_diag_prob_dist': io.c:371:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdialign.a gcc -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/dialign' Making all in Align make[4]: Entering directory '/build/abyss-2.1.5/Align' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Align' Making all in ABYSS make[4]: Entering directory '/build/abyss-2.1.5/ABYSS' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/ABYSS' Making all in Parallel make[4]: Entering directory '/build/abyss-2.1.5/Parallel' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Parallel' Making all in Bloom make[4]: Entering directory '/build/abyss-2.1.5/Bloom' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/abyss-2.1.5/BloomDBG' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/abyss-2.1.5/Konnector' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Konnector' Making all in Consensus make[4]: Entering directory '/build/abyss-2.1.5/Consensus' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Consensus' Making all in DAssembler make[4]: Entering directory '/build/abyss-2.1.5/DAssembler' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/abyss-2.1.5/DistanceEst' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-2.1.5/KAligner' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/KAligner' Making all in Layout make[4]: Entering directory '/build/abyss-2.1.5/Layout' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/abyss-2.1.5/LogKmerCount' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/LogKmerCount' Making all in Map make[4]: Entering directory '/build/abyss-2.1.5/Map' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Map' Making all in MergePaths make[4]: Entering directory '/build/abyss-2.1.5/MergePaths' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/MergePaths' Making all in Misc make[4]: Entering directory '/build/abyss-2.1.5/Misc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/Misc' Making all in Overlap make[4]: Entering directory '/build/abyss-2.1.5/Overlap' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/abyss-2.1.5/PairedDBG' g++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/abyss-2.1.5/ParseAligns' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm g++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-2.1.5/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-2.1.5/PathOverlap' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/abyss-2.1.5/PopBubbles' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/abyss-2.1.5/Scaffold' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/abyss-2.1.5/SimpleGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/abyss-2.1.5/kmerprint' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/abyss-2.1.5/FilterGraph' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/abyss-2.1.5/GapFiller' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/GapFiller' Making all in Sealer make[4]: Entering directory '/build/abyss-2.1.5/Sealer' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/Sealer' Making all in AdjList make[4]: Entering directory '/build/abyss-2.1.5/AdjList' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -Wall -Wextra -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/AdjList' Making all in lib/bloomfilter make[4]: Entering directory '/build/abyss-2.1.5/lib/bloomfilter' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/lib/bloomfilter' Making all in lib/nthash make[4]: Entering directory '/build/abyss-2.1.5/lib/nthash' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/lib/nthash' Making all in lib/gtest-1.7.0 make[4]: Entering directory '/build/abyss-2.1.5/lib/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/abyss-2.1.5/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-2.1.5/Unittest' make[4]: Entering directory '/build/abyss-2.1.5' make[4]: Leaving directory '/build/abyss-2.1.5' make[3]: Leaving directory '/build/abyss-2.1.5' make[2]: Leaving directory '/build/abyss-2.1.5' markdown_py -f README.html README.md make[1]: Leaving directory '/build/abyss-2.1.5' dh_auto_test make -j16 check VERBOSE=1 make[1]: Entering directory '/build/abyss-2.1.5' Making check in bin make[2]: Entering directory '/build/abyss-2.1.5/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/bin' Making check in doc make[2]: Entering directory '/build/abyss-2.1.5/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/doc' Making check in Common make[2]: Entering directory '/build/abyss-2.1.5/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Common' Making check in Graph make[2]: Entering directory '/build/abyss-2.1.5/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Graph' Making check in DataLayer make[2]: Entering directory '/build/abyss-2.1.5/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/DataLayer' Making check in DataBase make[2]: Entering directory '/build/abyss-2.1.5/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/DataBase' Making check in FMIndex make[2]: Entering directory '/build/abyss-2.1.5/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/FMIndex' Making check in Assembly make[2]: Entering directory '/build/abyss-2.1.5/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Assembly' Making check in dialign make[2]: Entering directory '/build/abyss-2.1.5/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/dialign' Making check in Align make[2]: Entering directory '/build/abyss-2.1.5/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Align' Making check in ABYSS make[2]: Entering directory '/build/abyss-2.1.5/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/ABYSS' Making check in Parallel make[2]: Entering directory '/build/abyss-2.1.5/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Parallel' Making check in Bloom make[2]: Entering directory '/build/abyss-2.1.5/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Bloom' Making check in BloomDBG make[2]: Entering directory '/build/abyss-2.1.5/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/BloomDBG' Making check in Konnector make[2]: Entering directory '/build/abyss-2.1.5/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Konnector' Making check in Consensus make[2]: Entering directory '/build/abyss-2.1.5/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Consensus' Making check in DAssembler make[2]: Entering directory '/build/abyss-2.1.5/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/abyss-2.1.5/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/abyss-2.1.5/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/KAligner' Making check in Layout make[2]: Entering directory '/build/abyss-2.1.5/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/abyss-2.1.5/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/LogKmerCount' Making check in Map make[2]: Entering directory '/build/abyss-2.1.5/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Map' Making check in MergePaths make[2]: Entering directory '/build/abyss-2.1.5/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/MergePaths' Making check in Misc make[2]: Entering directory '/build/abyss-2.1.5/Misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Misc' Making check in Overlap make[2]: Entering directory '/build/abyss-2.1.5/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Overlap' Making check in PairedDBG make[2]: Entering directory '/build/abyss-2.1.5/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/build/abyss-2.1.5/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/abyss-2.1.5/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/abyss-2.1.5/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/abyss-2.1.5/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/abyss-2.1.5/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/abyss-2.1.5/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/abyss-2.1.5/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/abyss-2.1.5/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/GapFiller' Making check in Sealer make[2]: Entering directory '/build/abyss-2.1.5/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/Sealer' Making check in AdjList make[2]: Entering directory '/build/abyss-2.1.5/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/AdjList' Making check in lib/bloomfilter make[2]: Entering directory '/build/abyss-2.1.5/lib/bloomfilter' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/lib/bloomfilter' Making check in lib/nthash make[2]: Entering directory '/build/abyss-2.1.5/lib/nthash' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-2.1.5/lib/nthash' Making check in lib/gtest-1.7.0 make[2]: Entering directory '/build/abyss-2.1.5/lib/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/build/abyss-2.1.5/lib/gtest-1.7.0' g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../lib/gtest-1.7.0/include -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -Wno-missing-field-initializers -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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-2.1.5/lib/gtest-1.7.0' make[2]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/abyss-2.1.5/Unittest' make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam 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_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer make[3]: Entering directory '/build/abyss-2.1.5/Unittest' g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerTest.o Common/KmerTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/Sequence.o Common/Sequence.cc g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../lib/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-2.1.5 -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/SAM.o Common/SAM.cc g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -Wall -Wextra -pthread -Wno-error -g -O2 -ffile-prefix-map=/build/abyss-2.1.5=. -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 ../lib/gtest-1.7.0/libgtest_main.a -ldl -lm make[3]: Leaving directory '/build/abyss-2.1.5/Unittest' make check-TESTS make[3]: Entering directory '/build/abyss-2.1.5/Unittest' make[4]: Entering directory '/build/abyss-2.1.5/Unittest' PASS: common_sequence PASS: common_histogram PASS: common_KmerIterator PASS: common_kmer PASS: common_bitutil PASS: common_stringutil PASS: Konnector_DBGBloom PASS: graph_BidirectionalBFS PASS: BloomFilter PASS: common_sam PASS: Konnector_DBGBloomAlgorithms PASS: graph_ConstrainedBFSVisitor PASS: graph_AllPathsSearch PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_HashGraph PASS: graph_ExtendPath PASS: graph_DotIO PASS: Konnector_konnector PASS: graph_UndirectedGraph PASS: BloomDBG_BloomDBG PASS: PairedDBG_KmerPair PASS: BloomDBG_HashAgnosticCascadingBloom PASS: PairedDBG_Dinuc PASS: BloomDBG_RollingHash PASS: BloomDBG_MaskedKmer PASS: BloomDBG_LightweightKmer PASS: PairedDBG_BranchRecord PASS: BloomDBG_SpacedSeed PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_RollingBloomDBG PASS: PairedDBG_LoadAlgorithm PASS: DBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.1.5 ============================================================================ # TOTAL: 32 # PASS: 32 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/abyss-2.1.5/Unittest' make[3]: Leaving directory '/build/abyss-2.1.5/Unittest' make[2]: Leaving directory '/build/abyss-2.1.5/Unittest' make[2]: Entering directory '/build/abyss-2.1.5' make[2]: Leaving directory '/build/abyss-2.1.5' make[1]: Leaving directory '/build/abyss-2.1.5' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-2.1.5' dh_auto_install --destdir=debian/tmp make -j16 install DESTDIR=/build/abyss-2.1.5/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-2.1.5' Making install in bin make[3]: Entering directory '/build/abyss-2.1.5/bin' make[4]: Entering directory '/build/abyss-2.1.5/bin' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-bowtie abyss-bowtie2 abyss-bwa abyss-bwasw abyss-bwamem abyss-fatoagp abyss-kaligner abyss-pe abyss-samtoafg abyss-tabtomd abyss-bloom-dist.mk abyss-dida abyss-stack-size '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/bin' make[3]: Leaving directory '/build/abyss-2.1.5/bin' Making install in doc make[3]: Entering directory '/build/abyss-2.1.5/doc' make[4]: Entering directory '/build/abyss-2.1.5/doc' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/build/abyss-2.1.5/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/build/abyss-2.1.5/doc' make[3]: Leaving directory '/build/abyss-2.1.5/doc' Making install in Common make[3]: Entering directory '/build/abyss-2.1.5/Common' make[4]: Entering directory '/build/abyss-2.1.5/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-2.1.5/Common' make[3]: Leaving directory '/build/abyss-2.1.5/Common' Making install in Graph make[3]: Entering directory '/build/abyss-2.1.5/Graph' make[4]: Entering directory '/build/abyss-2.1.5/Graph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Graph' make[3]: Leaving directory '/build/abyss-2.1.5/Graph' Making install in DataLayer make[3]: Entering directory '/build/abyss-2.1.5/DataLayer' make[4]: Entering directory '/build/abyss-2.1.5/DataLayer' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DataLayer' make[3]: Leaving directory '/build/abyss-2.1.5/DataLayer' Making install in DataBase make[3]: Entering directory '/build/abyss-2.1.5/DataBase' make[4]: Entering directory '/build/abyss-2.1.5/DataBase' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DataBase' make[3]: Leaving directory '/build/abyss-2.1.5/DataBase' Making install in FMIndex make[3]: Entering directory '/build/abyss-2.1.5/FMIndex' make[4]: Entering directory '/build/abyss-2.1.5/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-2.1.5/FMIndex' make[3]: Leaving directory '/build/abyss-2.1.5/FMIndex' Making install in Assembly make[3]: Entering directory '/build/abyss-2.1.5/Assembly' make[4]: Entering directory '/build/abyss-2.1.5/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-2.1.5/Assembly' make[3]: Leaving directory '/build/abyss-2.1.5/Assembly' Making install in dialign make[3]: Entering directory '/build/abyss-2.1.5/dialign' make[4]: Entering directory '/build/abyss-2.1.5/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-2.1.5/dialign' make[3]: Leaving directory '/build/abyss-2.1.5/dialign' Making install in Align make[3]: Entering directory '/build/abyss-2.1.5/Align' make[4]: Entering directory '/build/abyss-2.1.5/Align' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Align' make[3]: Leaving directory '/build/abyss-2.1.5/Align' Making install in ABYSS make[3]: Entering directory '/build/abyss-2.1.5/ABYSS' make[4]: Entering directory '/build/abyss-2.1.5/ABYSS' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/ABYSS' make[3]: Leaving directory '/build/abyss-2.1.5/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-2.1.5/Parallel' make[4]: Entering directory '/build/abyss-2.1.5/Parallel' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Parallel' make[3]: Leaving directory '/build/abyss-2.1.5/Parallel' Making install in Bloom make[3]: Entering directory '/build/abyss-2.1.5/Bloom' make[4]: Entering directory '/build/abyss-2.1.5/Bloom' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Bloom' make[3]: Leaving directory '/build/abyss-2.1.5/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/abyss-2.1.5/BloomDBG' make[4]: Entering directory '/build/abyss-2.1.5/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/BloomDBG' make[3]: Leaving directory '/build/abyss-2.1.5/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/abyss-2.1.5/Konnector' make[4]: Entering directory '/build/abyss-2.1.5/Konnector' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Konnector' make[3]: Leaving directory '/build/abyss-2.1.5/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-2.1.5/Consensus' make[4]: Entering directory '/build/abyss-2.1.5/Consensus' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Consensus' make[3]: Leaving directory '/build/abyss-2.1.5/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-2.1.5/DAssembler' make[4]: Entering directory '/build/abyss-2.1.5/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DAssembler' make[3]: Leaving directory '/build/abyss-2.1.5/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/abyss-2.1.5/DistanceEst' make[4]: Entering directory '/build/abyss-2.1.5/DistanceEst' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/DistanceEst' make[3]: Leaving directory '/build/abyss-2.1.5/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/abyss-2.1.5/KAligner' make[4]: Entering directory '/build/abyss-2.1.5/KAligner' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/KAligner' make[3]: Leaving directory '/build/abyss-2.1.5/KAligner' Making install in Layout make[3]: Entering directory '/build/abyss-2.1.5/Layout' make[4]: Entering directory '/build/abyss-2.1.5/Layout' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Layout' make[3]: Leaving directory '/build/abyss-2.1.5/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-2.1.5/LogKmerCount' make[4]: Entering directory '/build/abyss-2.1.5/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/LogKmerCount' make[3]: Leaving directory '/build/abyss-2.1.5/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-2.1.5/Map' make[4]: Entering directory '/build/abyss-2.1.5/Map' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Map' make[3]: Leaving directory '/build/abyss-2.1.5/Map' Making install in MergePaths make[3]: Entering directory '/build/abyss-2.1.5/MergePaths' make[4]: Entering directory '/build/abyss-2.1.5/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/MergePaths' make[3]: Leaving directory '/build/abyss-2.1.5/MergePaths' Making install in Misc make[3]: Entering directory '/build/abyss-2.1.5/Misc' make[4]: Entering directory '/build/abyss-2.1.5/Misc' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-2.1.5/Misc' make[3]: Leaving directory '/build/abyss-2.1.5/Misc' Making install in Overlap make[3]: Entering directory '/build/abyss-2.1.5/Overlap' make[4]: Entering directory '/build/abyss-2.1.5/Overlap' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Overlap' make[3]: Leaving directory '/build/abyss-2.1.5/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/abyss-2.1.5/PairedDBG' make[4]: Entering directory '/build/abyss-2.1.5/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/PairedDBG' make[3]: Leaving directory '/build/abyss-2.1.5/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-2.1.5/ParseAligns' make[4]: Entering directory '/build/abyss-2.1.5/ParseAligns' /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/ParseAligns' make[3]: Leaving directory '/build/abyss-2.1.5/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-2.1.5/PathOverlap' make[4]: Entering directory '/build/abyss-2.1.5/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/PathOverlap' make[3]: Leaving directory '/build/abyss-2.1.5/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-2.1.5/PopBubbles' make[4]: Entering directory '/build/abyss-2.1.5/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/PopBubbles' make[3]: Leaving directory '/build/abyss-2.1.5/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-2.1.5/Scaffold' make[4]: Entering directory '/build/abyss-2.1.5/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Scaffold' make[3]: Leaving directory '/build/abyss-2.1.5/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/abyss-2.1.5/SimpleGraph' make[4]: Entering directory '/build/abyss-2.1.5/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/SimpleGraph' make[3]: Leaving directory '/build/abyss-2.1.5/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/abyss-2.1.5/kmerprint' make[4]: Entering directory '/build/abyss-2.1.5/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-2.1.5/kmerprint' make[3]: Leaving directory '/build/abyss-2.1.5/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/abyss-2.1.5/FilterGraph' make[4]: Entering directory '/build/abyss-2.1.5/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/FilterGraph' make[3]: Leaving directory '/build/abyss-2.1.5/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/abyss-2.1.5/GapFiller' make[4]: Entering directory '/build/abyss-2.1.5/GapFiller' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/GapFiller' make[3]: Leaving directory '/build/abyss-2.1.5/GapFiller' Making install in Sealer make[3]: Entering directory '/build/abyss-2.1.5/Sealer' make[4]: Entering directory '/build/abyss-2.1.5/Sealer' /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/Sealer' make[3]: Leaving directory '/build/abyss-2.1.5/Sealer' Making install in AdjList make[3]: Entering directory '/build/abyss-2.1.5/AdjList' make[4]: Entering directory '/build/abyss-2.1.5/AdjList' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/abyss-2.1.5/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-2.1.5/AdjList' make[3]: Leaving directory '/build/abyss-2.1.5/AdjList' Making install in lib/bloomfilter make[3]: Entering directory '/build/abyss-2.1.5/lib/bloomfilter' make[4]: Entering directory '/build/abyss-2.1.5/lib/bloomfilter' 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-2.1.5/lib/bloomfilter' make[3]: Leaving directory '/build/abyss-2.1.5/lib/bloomfilter' Making install in lib/nthash make[3]: Entering directory '/build/abyss-2.1.5/lib/nthash' make[4]: Entering directory '/build/abyss-2.1.5/lib/nthash' 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-2.1.5/lib/nthash' make[3]: Leaving directory '/build/abyss-2.1.5/lib/nthash' Making install in lib/gtest-1.7.0 make[3]: Entering directory '/build/abyss-2.1.5/lib/gtest-1.7.0' make[4]: Entering directory '/build/abyss-2.1.5/lib/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-2.1.5/lib/gtest-1.7.0' make[3]: Leaving directory '/build/abyss-2.1.5/lib/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/abyss-2.1.5/Unittest' make[4]: Entering directory '/build/abyss-2.1.5/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-2.1.5/Unittest' make[3]: Leaving directory '/build/abyss-2.1.5/Unittest' make[3]: Entering directory '/build/abyss-2.1.5' make[4]: Entering directory '/build/abyss-2.1.5' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/abyss-2.1.5/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-2.1.5' make[3]: Leaving directory '/build/abyss-2.1.5' make[2]: Leaving directory '/build/abyss-2.1.5' 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-2.1.5' debian/rules override_dh_install make[1]: Entering directory '/build/abyss-2.1.5' 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-2.1.5' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.1.5-7_amd64.deb'. dpkg-deb: building package 'abyss' in '../abyss_2.1.5-7_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../abyss_2.1.5-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/2150296 and its subdirectories I: Current time: Sun Jan 1 02:14:32 -12 2023 I: pbuilder-time-stamp: 1672582472 Mon Nov 29 07:51:29 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Mon Nov 29 07:51:29 UTC 2021 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Mon Nov 29 08:10:58 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Mon Nov 29 08:10:58 UTC 2021 I: abyss_2.1.5-7_amd64.changes: Format: 1.8 Date: Sun, 17 Feb 2019 05:19:54 -0800 Source: abyss Binary: abyss abyss-dbgsym Architecture: amd64 Version: 2.1.5-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (2.1.5-7) unstable; urgency=medium . * Add myself as an uploader. * The package openmpi-bin is now a required dependency for the abyss binary package. Many thanks to ci.debian.org for bringing this to light. * Fix "implicit declaration of function"s in dialign/museq.c * Fix some spelling typos * Register the flowchart PDFs with doc-base Checksums-Sha1: d657985e764346460d50fe282a894e1c5fde2b6f 29559272 abyss-dbgsym_2.1.5-7_amd64.deb c8ddf9be709b764196e8a8f0a3498fdfb60d7865 7416 abyss_2.1.5-7_amd64.buildinfo 61c7785f5fcfec4bcc872e3f724378c7e4fe86a0 2952944 abyss_2.1.5-7_amd64.deb Checksums-Sha256: aba815cb6cc7b55e46cf6e08c76480f64b40465268571d7bd3dff8041f132a5e 29559272 abyss-dbgsym_2.1.5-7_amd64.deb f577c175aa1b0fd60957ea73c7834f8af2aadda9f07551a9a206dded190adbeb 7416 abyss_2.1.5-7_amd64.buildinfo 2adfffadff85cda9e6a7270bdddb5801b2d63cd60af1e1b96c09fbb377ecea67 2952944 abyss_2.1.5-7_amd64.deb Files: 5bde80249094913eb0193c967665bfda 29559272 debug optional abyss-dbgsym_2.1.5-7_amd64.deb 0588ed4e632d44534c3d0be54b863ee7 7416 science optional abyss_2.1.5-7_amd64.buildinfo db564b11ef520202ceb80ab430af5d9c 2952944 science optional abyss_2.1.5-7_amd64.deb Mon Nov 29 08:10:59 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.7CccSBudTb/abyss_2.1.5-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.7CccSBudTb/abyss_2.1.5-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.7CccSBudTb/abyss_2.1.5-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.7CccSBudTb/b1/abyss_2.1.5-7_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.7CccSBudTb/b2/abyss_2.1.5-7_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.585s) 0.585s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.372s) 0.372s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Mon Nov 29 08:11:00 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Mon Nov 29 08:11:00 UTC 2021 I: abyss from buster built successfully and reproducibly on amd64. Mon Nov 29 08:11:02 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Nov 29 08:11:02 UTC 2021 I: Submitting 12K b1/abyss_2.1.5-7_amd64.buildinfo.asc Mon Nov 29 08:11:03 UTC 2021 I: Submitting 12K b2/abyss_2.1.5-7_amd64.buildinfo.asc Mon Nov 29 08:11:03 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Nov 29 08:11:03 UTC 2021 I: Done submitting .buildinfo files. Mon Nov 29 08:11:03 UTC 2021 I: Removing signed abyss_2.1.5-7_amd64.buildinfo.asc files: removed './b1/abyss_2.1.5-7_amd64.buildinfo.asc' removed './b2/abyss_2.1.5-7_amd64.buildinfo.asc'