Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/a/abyss/abyss_2.2.5+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/abyss-2.2.5+dfsg-1sd9or_oj/abyss_2.2.5+dfsg-1_amd64.buildinfo Get source package info: abyss=2.2.5+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/abyss/2.2.5+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.69-11.1 automake=1:1.16.3-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc3-1 binutils=2.35.1-3 binutils-common=2.35.1-3 binutils-x86-64-linux-gnu=2.35.1-3 bsdextrautils=2.36.1-2 bsdutils=1:2.36.1-2 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-23 cpp-9=9.3.0-19 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.39-3 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-23 gcc=4:10.2.0-1 gcc-10=10.2.0-23 gcc-10-base=10.2.0-23 gcc-9=9.3.0-19 gcc-9-base=9.3.0-19 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 gfortran-9=9.3.0-19 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 help2man=1.47.16 hostname=3.23 ibverbs-providers=32.0-1+b1 icu-devtools=67.1-4 init-system-helpers=1.59 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan5=9.3.0-19 libasan6=10.2.0-23 libatomic1=10.2.0-23 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbinutils=2.35.1-3 libblkid1=2.36.1-2 libboost-graph-dev=1.71.0.3 libboost-graph1.71-dev=1.71.0-7+b1 libboost-graph1.71.0=1.71.0-7+b1 libboost-regex1.71-dev=1.71.0-7+b1 libboost-regex1.71.0=1.71.0-7+b1 libboost-serialization1.71-dev=1.71.0-7+b1 libboost-serialization1.71.0=1.71.0-7+b1 libboost-test1.71-dev=1.71.0-7+b1 libboost-test1.71.0=1.71.0-7+b1 libboost1.71-dev=1.71.0-7+b1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-4 libc-bin=2.31-5 libc-dev-bin=2.31-5 libc6=2.31-5 libc6-dev=2.31-5 libcap-ng0=0.7.9-2.2+b1 libcbor0=0.5.0+dfsg-2 libcc1-0=10.2.0-23 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-3 libctf0=2.35.1-3 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdpkg-perl=1.20.5 libedit2=3.1-20191231-1 libelf1=0.182-1 libevent-2.1-7=2.1.12-stable-1 libevent-core-2.1-7=2.1.12-stable-1 libevent-dev=2.1.12-stable-1 libevent-extra-2.1-7=2.1.12-stable-1 libevent-openssl-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libfabric1=1.11.0-2 libffi7=3.3-5 libfido2-1=1.5.0-2 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-23 libgcc-9-dev=9.3.0-19 libgcc-s1=10.2.0-23 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran-9-dev=9.3.0-19 libgfortran5=10.2.0-23 libglib2.0-0=2.66.3-2 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.0-23 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libhtml-parser-perl=3.75-1+b1 libhtml-tagset-perl=3.20-4 libhwloc-dev=2.4.0+dfsg-2 libhwloc-plugins=2.4.0+dfsg-2 libhwloc15=2.4.0+dfsg-2 libibverbs-dev=32.0-1+b1 libibverbs1=32.0-1+b1 libicu-dev=67.1-4 libicu67=67.1-4 libisl23=0.23-1 libitm1=10.2.0-23 libjs-jquery=3.5.1+dfsg+~3.5.4-3 libjs-jquery-ui=1.12.1+dfsg-7 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.0-23 libltdl-dev=2.4.6-14 libltdl7=2.4.6-14 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnl-3-200=3.4.0-1+b1 libnl-3-dev=3.4.0-1+b1 libnl-route-3-200=3.4.0-1+b1 libnl-route-3-dev=3.4.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.12-1+b1 libnuma1=2.0.12-1+b1 libopenmpi-dev=4.0.5-7 libopenmpi3=4.0.5-7 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpciaccess0=0.16-1 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libpmix-dev=3.2.1-1 libpmix2=3.2.1-1 libpsm-infinipath1=3.3+20.604758e7-6+b1 libpsm2-2=11.2.185-1 libquadmath0=10.2.0-23 librdmacm1=32.0-1+b1 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsemanage-common=3.1-1 libsemanage1=3.1-1+b1 libsepol1=3.1-1 libsigsegv2=2.12-2 libsmartcols1=2.36.1-2 libsparsehash-dev=2.0.3-2 libsqlite3-0=3.33.0-1 libsqlite3-dev=3.33.0-1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-23 libstdc++6=10.2.0-23 libsub-override-perl=0.09-2 libsystemd0=246.6-5 libtext-markdown-perl=1.000031-3 libtext-multimarkdown-perl=1.000035-2 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.0-23 libubsan1=10.2.0-23 libuchardet0=0.0.7-1 libucx0=1.9.0~rc1-2 libudev1=246.6-5 libunistring2=0.9.10-4 liburi-perl=5.05-1 libuuid1=2.36.1-2 libx11-6=2:1.6.12-1 libx11-data=2:1.6.12-1 libxau6=1:1.0.8-1+b2 libxcb1=1.14-2 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.3-1+b2 libxml2=2.9.10+dfsg-6.3 libxnvctrl0=450.80.02-1 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.11-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-1 ncurses-bin=6.2+20201114-1 node-jquery=3.5.1+dfsg+~3.5.4-3 ocl-icd-libopencl1=2.2.13-1 openmpi-bin=4.0.5-7 openmpi-common=4.0.5-7 openssh-client=1:8.4p1-3 passwd=1:4.8.1-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 pkg-config=0.29.2-1 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 util-linux=2.36.1-2 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201208T030340Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201202T205335Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d abyss=2.2.5+dfsg-1 && mkdir -p /build/abyss-osip9F && dpkg-source --no-check -x /*.dsc /build/abyss-osip9F/abyss-2.2.5+dfsg && chown -R builduser:builduser /build/abyss-osip9F" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/abyss-osip9F/abyss-2.2.5+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607089354" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/abyss-osip9F /tmp/abyss-2.2.5+dfsg-1sd9or_oj bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201202T205335Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.ffX04ahAQx as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.ffX04ahAQx Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-2). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201202T205335Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201202T205335Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1074 kB/s) Selecting previously unselected package libfakeroot: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 ... 4614 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-5) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201208T030340Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201202T205335Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.ffX04ahAQx Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201208T030340Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201202T205335Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20201208T030340Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201208T030340Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20201208T030340Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20201208T030340Z unstable/main amd64 Packages [11.6 MB] Fetched 34.3 MB in 30s (1135 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.ffX04ahAQx I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d abyss=2.2.5+dfsg-1 && mkdir -p /build/abyss-osip9F && dpkg-source --no-check -x /*.dsc /build/abyss-osip9F/abyss-2.2.5+dfsg && chown -R builduser:builduser /build/abyss-osip9F"' exec /tmp/mmdebstrap.ffX04ahAQx Reading package lists... NOTICE: 'abyss' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/abyss.git Please use: git clone https://salsa.debian.org/med-team/abyss.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1798 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main abyss 2.2.5+dfsg-1 (dsc) [2371 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main abyss 2.2.5+dfsg-1 (tar) [1042 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main abyss 2.2.5+dfsg-1 (diff) [754 kB] Fetched 1798 kB in 2s (1179 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'abyss_2.2.5+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting abyss in /build/abyss-osip9F/abyss-2.2.5+dfsg dpkg-source: info: unpacking abyss_2.2.5+dfsg.orig.tar.xz dpkg-source: info: unpacking abyss_2.2.5+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/abyss-osip9F/abyss-2.2.5+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607089354" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.ffX04ahAQx dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.2.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:25: installing './ar-lib' configure.ac:16: installing './compile' configure.ac:167: installing './config.guess' configure.ac:167: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' dh_auto_configure -- \ --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether g++ supports C++11 features with -std=c++11... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of g++ -std=c++11... none checking for gawk... (cached) mawk checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ -std=c++11 accepts -g... (cached) yes checking for ranlib... ranlib checking for ghc... no ./configure: line 5926: : command not found checking for pandoc... no checking for ar... ar checking the archiver (ar) interface... ar checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for ANSI C header files... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for std::hash... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... yes checking for dup2... yes checking for gethostname... yes checking for getopt_long... yes checking for getpagesize... yes checking for memset... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for vprintf... yes checking for _doprnt... no checking whether HOST_NAME_MAX is declared... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking how to run the C++ preprocessor... g++ -std=c++11 -E checking functional usability... yes checking functional presence... yes checking for functional... yes checking tr1/functional usability... yes checking tr1/functional presence... yes checking for tr1/functional... yes checking boost/functional/hash.hpp usability... yes checking boost/functional/hash.hpp presence... yes checking for boost/functional/hash.hpp... yes checking boost/property_map/property_map.hpp usability... yes checking boost/property_map/property_map.hpp presence... yes checking for boost/property_map/property_map.hpp... yes checking google/sparse_hash_map usability... yes checking google/sparse_hash_map presence... yes checking for google/sparse_hash_map... yes checking unordered_map usability... yes checking unordered_map presence... yes checking for unordered_map... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking unordered_set usability... yes checking unordered_set presence... yes checking for unordered_set... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking boost/unordered_set.hpp usability... yes checking boost/unordered_set.hpp presence... yes checking for boost/unordered_set.hpp... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for g++ -std=c++11 option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating vendor/gtest-1.7.0/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating vendor/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' dh_auto_build make -j4 make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' make all-recursive make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' Making all in bin make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/bin' Making all in doc make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/doc' Making all in Common make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc rm -f libcommon.a ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcommon.a make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Common' Making all in Graph make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Graph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L. -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Graph' Making all in DataLayer make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc rm -f libdatalayer.a ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc rm -f libfmindex.a ar cru libfmindex.a libfmindex_a-bit_array.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfmindex.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FMIndex' Making all in Assembly make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc rm -f libassembly.a ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libassembly.a make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Assembly' Making all in dialign make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c alig.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ assemble.c:40:20: warning: inline function ‘align_diag’ declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never defined 37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); | ^~~~~~~~ assemble.c:25:39: warning: inline function ‘find_diags_guided’ declared but never defined 25 | extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, | ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ diag.c:1456:3: warning: ‘real_calc_weight’ is static but used in inline function ‘find_diags_dyn’ which is not static 1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); | ^~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c io.c: In function ‘read_scr_matrix’: io.c:270:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 270 | fscanf( fp, "%i", &is); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:282:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 282 | fscanf(fp, "%s\n", rline); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘read_diag_prob_dist’: io.c:371:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdialign.a gcc -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/dialign' Making all in Align make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Align' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc rm -f libalign.a ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libalign.a g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Align' Making all in ABYSS make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ABYSS' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ABYSS' Making all in Parallel make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Parallel' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Parallel' Making all in Bloom make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Bloom' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/BloomDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Konnector' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Konnector' Making all in Consensus make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Consensus' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Consensus' Making all in DAssembler make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DAssembler' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DistanceEst' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/KAligner' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/KAligner' Making all in Layout make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Layout' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/LogKmerCount' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/LogKmerCount' Making all in Map make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Map' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Map' Making all in MergePaths make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/MergePaths' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/MergePaths' Making all in Overlap make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Overlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PairedDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KmerPair.o KmerPair.cc rm -f libpaireddbg.a ar cru libpaireddbg.a KmerPair.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpaireddbg.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ParseAligns' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PathOverlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PopBubbles' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Scaffold' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/SimpleGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/kmerprint' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FilterGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/GapFiller' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/GapFiller' Making all in Sealer make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Sealer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Sealer' Making all in AdjList make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/AdjList' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/AdjList' Making all in vendor make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' markdown README.md > README.html make[1]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' dh_auto_test -a make -j4 check VERBOSE=1 make[1]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' Making check in bin make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/bin' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/bin' Making check in doc make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/doc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/doc' Making check in Common make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Common' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Common' Making check in Graph make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Graph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Graph' Making check in DataLayer make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataLayer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataLayer' Making check in DataBase make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataBase' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataBase' Making check in FMIndex make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FMIndex' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FMIndex' Making check in Assembly make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Assembly' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Assembly' Making check in dialign make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/dialign' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/dialign' Making check in Align make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Align' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Align' Making check in ABYSS make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ABYSS' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ABYSS' Making check in Parallel make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Parallel' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Parallel' Making check in Bloom make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Bloom' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Bloom' Making check in BloomDBG make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/BloomDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/BloomDBG' Making check in Konnector make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Konnector' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Konnector' Making check in Consensus make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Consensus' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Consensus' Making check in DAssembler make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DAssembler' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DAssembler' Making check in DistanceEst make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DistanceEst' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DistanceEst' Making check in KAligner make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/KAligner' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/KAligner' Making check in Layout make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Layout' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Layout' Making check in LogKmerCount make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/LogKmerCount' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/LogKmerCount' Making check in Map make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Map' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Map' Making check in MergePaths make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/MergePaths' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/MergePaths' Making check in Overlap make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Overlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Overlap' Making check in PairedDBG make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PairedDBG' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PairedDBG' Making check in ParseAligns make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ParseAligns' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ParseAligns' Making check in PathOverlap make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PathOverlap' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PathOverlap' Making check in PopBubbles make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PopBubbles' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PopBubbles' Making check in Scaffold make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Scaffold' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Scaffold' Making check in SimpleGraph make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/SimpleGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/SimpleGraph' Making check in kmerprint make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/kmerprint' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/kmerprint' Making check in FilterGraph make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FilterGraph' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FilterGraph' Making check in GapFiller make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/GapFiller' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/GapFiller' Making check in Sealer make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Sealer' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Sealer' Making check in AdjList make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/AdjList' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/AdjList' Making check in vendor make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor' Making check in vendor/gtest-1.7.0 make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' make libgtest.a libgtest_main.a make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../.. -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc rm -f libgtest_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 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 make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' Making check in Unittest make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make common_stringutil common_histogram common_bitutil common_kmer common_sequence common_KmerIterator common_sam common_sam_ssq BloomFilter Konnector_DBGBloom Konnector_DBGBloomAlgorithms graph_ConstrainedBFSVisitor graph_BidirectionalBFS graph_AllPathsSearch graph_HashGraph graph_ConstrainedBidiBFSVisitor graph_ExtendPath graph_DotIO graph_UndirectedGraph Konnector_konnector DBG_LoadAlgorithm PairedDBG_LoadAlgorithm PairedDBG_KmerPair PairedDBG_Dinuc PairedDBG_BranchRecord BloomDBG_BloomDBG BloomDBG_RollingHash BloomDBG_RollingHashIterator BloomDBG_HashAgnosticCascadingBloom BloomDBG_CountingBloomFilter BloomDBG_RollingBloomDBG BloomDBG_MaskedKmer BloomDBG_SpacedSeed BloomDBG_LightweightKmer make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/konnector-konnectorTest.o `test -f 'Konnector/konnectorTest.cpp' || echo './'`Konnector/konnectorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/StringUtilTest.o Common/StringUtilTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/HistogramTest.o Common/HistogramTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/BitUtilTest.o Common/BitUtilTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerTest.o Common/KmerTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/Sequence.o Common/Sequence.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/KmerIteratorTest.o Common/KmerIteratorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/SAM.o Common/SAM.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -DSAM_SEQ_QUAL -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Common/common_sam_ssq-SAM.o `test -f 'Common/SAM.cc' || echo './'`Common/SAM.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/BloomFilter-BloomFilter.o `test -f 'Konnector/BloomFilter.cc' || echo './'`Konnector/BloomFilter.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloom-DBGBloomTest.o `test -f 'Konnector/DBGBloomTest.cpp' || echo './'`Konnector/DBGBloomTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o `test -f 'Konnector/DBGBloomAlgorithmsTest.cpp' || echo './'`Konnector/DBGBloomAlgorithmsTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o `test -f 'Graph/ConstrainedBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBFSVisitorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o `test -f 'Graph/BidirectionalBFSTest.cpp' || echo './'`Graph/BidirectionalBFSTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_AllPathsSearch-AllPathsSearchTest.o `test -f 'Graph/AllPathsSearchTest.cpp' || echo './'`Graph/AllPathsSearchTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_HashGraph-HashGraphTest.o `test -f 'Graph/HashGraphTest.cpp' || echo './'`Graph/HashGraphTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o `test -f 'Graph/ConstrainedBidiBFSVisitorTest.cpp' || echo './'`Graph/ConstrainedBidiBFSVisitorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_ExtendPath-ExtendPathTest.o `test -f 'Graph/ExtendPathTest.cpp' || echo './'`Graph/ExtendPathTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/graph_DotIO-DotIOTest.o `test -f 'Graph/DotIOTest.cpp' || echo './'`Graph/DotIOTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Graph/UndirectedGraphTest.o Graph/UndirectedGraphTest.cpp g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_konnector Konnector/konnector-konnectorTest.o ../Align/libalign.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'DBG/LoadAlgorithmTest.cpp' || echo './'`DBG/LoadAlgorithmTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o `test -f 'PairedDBG/LoadAlgorithmTest.cpp' || echo './'`PairedDBG/LoadAlgorithmTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/KmerPair-KmerPairTest.o `test -f 'PairedDBG/KmerPairTest.cc' || echo './'`PairedDBG/KmerPairTest.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/Dinuc-DinucTest.o `test -f 'PairedDBG/DinucTest.cc' || echo './'`PairedDBG/DinucTest.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../DataLayer -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PairedDBG/BranchRecord-BranchRecordTest.o `test -f 'PairedDBG/BranchRecordTest.cpp' || echo './'`PairedDBG/BranchRecordTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/BloomDBG-BloomDBGTest.o `test -f 'BloomDBG/BloomDBGTest.cpp' || echo './'`BloomDBG/BloomDBGTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashTest.o BloomDBG/RollingHashTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingHashIteratorTest.o BloomDBG/RollingHashIteratorTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o `test -f 'BloomDBG/HashAgnosticCascadingBloomTest.cpp' || echo './'`BloomDBG/HashAgnosticCascadingBloomTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I../Common -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o `test -f 'BloomDBG/CountingBloomFilterTest.cpp' || echo './'`BloomDBG/CountingBloomFilterTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o `test -f 'BloomDBG/RollingBloomDBGTest.cpp' || echo './'`BloomDBG/RollingBloomDBGTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/MaskedKmerTest.o BloomDBG/MaskedKmerTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/SpacedSeedTest.o BloomDBG/SpacedSeedTest.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../vendor/gtest-1.7.0/include -DGTEST_USE_OWN_TR1_TUPLE=0 -I/build/abyss-osip9F/abyss-2.2.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-osip9F/abyss-2.2.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o BloomDBG/LightweightKmerTest.o BloomDBG/LightweightKmerTest.cpp g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_stringutil Common/StringUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_histogram Common/HistogramTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_bitutil Common/BitUtilTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_kmer Common/KmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sequence Common/Sequence.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_KmerIterator Common/KmerIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam Common/SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o common_sam_ssq Common/common_sam_ssq-SAM.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomFilter Konnector/BloomFilter-BloomFilter.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloom Konnector/DBGBloom-DBGBloomTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Konnector_DBGBloomAlgorithms Konnector/DBGBloomAlgorithms-DBGBloomAlgorithmsTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBFSVisitor Graph/graph_ConstrainedBFSVisitor-ConstrainedBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_AllPathsSearch Graph/graph_AllPathsSearch-AllPathsSearchTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_BidirectionalBFS Graph/graph_BidirectionalBFS-BidirectionalBFSTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_HashGraph Graph/graph_HashGraph-HashGraphTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ConstrainedBidiBFSVisitor Graph/graph_ConstrainedBidiBFSVisitor-ConstrainedBidiBFSVisitorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_ExtendPath Graph/graph_ExtendPath-ExtendPathTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_DotIO Graph/graph_DotIO-DotIOTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o graph_UndirectedGraph Graph/UndirectedGraphTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DBG_LoadAlgorithm DBG/LoadAlgorithm-LoadAlgorithmTest.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_LoadAlgorithm PairedDBG/LoadAlgorithm-LoadAlgorithmTest.o ../PairedDBG/libpaireddbg.a ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_KmerPair PairedDBG/KmerPair-KmerPairTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_Dinuc PairedDBG/Dinuc-DinucTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PairedDBG_BranchRecord PairedDBG/BranchRecord-BranchRecordTest.o ../PairedDBG/libpaireddbg.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_BloomDBG BloomDBG/BloomDBG-BloomDBGTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHash BloomDBG/RollingHashTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingHashIterator BloomDBG/RollingHashIteratorTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_HashAgnosticCascadingBloom BloomDBG/HashAgnosticCascadingBloom-HashAgnosticCascadingBloomTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_CountingBloomFilter BloomDBG/CountingBloomFilter-CountingBloomFilterTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_MaskedKmer BloomDBG/MaskedKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_SpacedSeed BloomDBG/SpacedSeedTest.o ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_LightweightKmer BloomDBG/LightweightKmerTest.o ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -pthread -Wno-error -fopenmp -g -O2 -fdebug-prefix-map=/build/abyss-osip9F/abyss-2.2.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o BloomDBG_RollingBloomDBG BloomDBG/RollingBloomDBG-RollingBloomDBGTest.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../vendor/gtest-1.7.0/libgtest_main.a -ldl -lm make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make check-TESTS make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' PASS: common_kmer PASS: common_stringutil PASS: common_histogram PASS: common_bitutil PASS: common_sequence PASS: common_KmerIterator PASS: common_sam_ssq PASS: common_sam PASS: BloomFilter PASS: Konnector_DBGBloomAlgorithms PASS: Konnector_DBGBloom PASS: graph_ConstrainedBFSVisitor PASS: graph_BidirectionalBFS PASS: graph_AllPathsSearch PASS: graph_HashGraph PASS: graph_ConstrainedBidiBFSVisitor PASS: graph_DotIO PASS: graph_UndirectedGraph PASS: Konnector_konnector PASS: graph_ExtendPath PASS: PairedDBG_KmerPair PASS: PairedDBG_Dinuc PASS: PairedDBG_BranchRecord PASS: BloomDBG_BloomDBG PASS: BloomDBG_RollingHash PASS: BloomDBG_RollingHashIterator PASS: BloomDBG_HashAgnosticCascadingBloom PASS: BloomDBG_CountingBloomFilter PASS: BloomDBG_RollingBloomDBG PASS: BloomDBG_MaskedKmer PASS: BloomDBG_SpacedSeed PASS: BloomDBG_LightweightKmer PASS: DBG_LoadAlgorithm PASS: PairedDBG_LoadAlgorithm ============================================================================ Testsuite summary for ABySS 2.2.5 ============================================================================ # TOTAL: 34 # PASS: 34 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' make[1]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' dh_auto_install --destdir=debian/tmp make -j4 install DESTDIR=/build/abyss-osip9F/abyss-2.2.5\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' Making install in bin make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/bin' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/bin' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/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-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/bin' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/bin' Making install in doc make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/doc' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/doc' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ABYSS.1 abyss-pe.1 abyss-tofastq.1 '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/share/man/man1' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/doc' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/doc' Making install in Common make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Common' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Common' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Common' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Common' Making install in Graph make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Graph' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Graph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Graph' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Graph' Making install in DataLayer make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataLayer' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataLayer' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataLayer' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataLayer' Making install in DataBase make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataBase' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataBase' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataBase' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DataBase' Making install in FMIndex make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FMIndex' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FMIndex' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FMIndex' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FMIndex' Making install in Assembly make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Assembly' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Assembly' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Assembly' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Assembly' Making install in dialign make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/dialign' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/dialign' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/dialign' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/dialign' Making install in Align make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Align' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Align' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Align' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Align' Making install in ABYSS make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ABYSS' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ABYSS' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c ABYSS '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ABYSS' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Parallel' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Parallel' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Parallel' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Parallel' Making install in Bloom make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Bloom' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Bloom' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Bloom' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/BloomDBG' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/BloomDBG' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Konnector' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Konnector' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Konnector' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Consensus' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Consensus' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c Consensus '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Consensus' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DAssembler' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DAssembler' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DistanceEst' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DistanceEst' /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DistanceEst' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/KAligner' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/KAligner' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c KAligner '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/KAligner' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/KAligner' Making install in Layout make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Layout' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Layout' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-layout '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Layout' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/LogKmerCount' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/LogKmerCount' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c logcounter '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/LogKmerCount' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Map' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Map' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Map' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Map' Making install in MergePaths make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/MergePaths' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/MergePaths' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/MergePaths' Making install in Overlap make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Overlap' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Overlap' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Overlap' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PairedDBG' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PairedDBG' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-paired-dbg '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PairedDBG' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ParseAligns' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ParseAligns' /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/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-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ParseAligns' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PathOverlap' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PathOverlap' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PopBubbles' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PopBubbles' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Scaffold' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Scaffold' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/SimpleGraph' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/SimpleGraph' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/kmerprint' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/kmerprint' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/kmerprint' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FilterGraph' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FilterGraph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-filtergraph '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FilterGraph' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/GapFiller' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/GapFiller' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-gapfill '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/GapFiller' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/GapFiller' Making install in Sealer make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Sealer' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Sealer' /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Sealer' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Sealer' Making install in AdjList make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/AdjList' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/AdjList' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c AdjList '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/AdjList' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/AdjList' Making install in vendor make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/vendor/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg/Unittest' make[3]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' make[4]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/abyss-osip9F/abyss-2.2.5+dfsg/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' make[3]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' make[2]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin 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/sbin:/usr/bin:/sbin:/bin 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-osip9F/abyss-2.2.5+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/abyss-osip9F/abyss-2.2.5+dfsg' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.2.5+dfsg-1_amd64.deb'. dpkg-deb: building package 'abyss' in '../abyss_2.2.5+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../abyss_2.2.5+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/abyss-osip9F /tmp/abyss-2.2.5+dfsg-1sd9or_oj I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.ffX04ahAQx... I: success in 2139.5555 seconds md5: abyss-dbgsym_2.2.5+dfsg-1_amd64.deb: OK md5: abyss_2.2.5+dfsg-1_amd64.deb: OK sha1: abyss-dbgsym_2.2.5+dfsg-1_amd64.deb: OK sha1: abyss_2.2.5+dfsg-1_amd64.deb: OK sha256: abyss-dbgsym_2.2.5+dfsg-1_amd64.deb: OK sha256: abyss_2.2.5+dfsg-1_amd64.deb: OK Checksums: OK