Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/a/abyss/abyss_2.3.5+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/abyss-2.3.5+dfsg-1nitusb7w/abyss_2.3.5+dfsg-1_amd64.buildinfo Get source package info: abyss=2.3.5+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/abyss/2.3.5+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.121 autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6+b1 binutils=2.38-4 binutils-common=2.38-4 binutils-x86-64-linux-gnu=2.38-4 bsdextrautils=2.38-4 bsdutils=1:2.38-4 build-essential=12.9 bzip2=1.0.8-5 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.3.0-1 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.7.1 debianutils=5.7-0.2 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 file=1:5.41-4 findutils=4.9.0-3 g++=4:11.2.0-2 g++-11=11.3.0-1 gcc=4:11.2.0-2 gcc-11=11.3.0-1 gcc-11-base=11.3.0-1 gcc-12-base=12.1.0-2 gettext=0.21-6 gettext-base=0.21-6 gfortran-11=11.3.0-1 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 help2man=1.49.2 hostname=3.23 ibverbs-providers=39.0-1+b1 icu-devtools=71.1-3 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.3.0-1 libatomic1=12.1.0-2 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-4 libblkid1=2.38-4 libboost-graph-dev=1.74.0.3 libboost-graph1.74-dev=1.74.0-14+b1 libboost-graph1.74.0=1.74.0-14+b1 libboost-regex1.74-dev=1.74.0-14+b1 libboost-regex1.74.0=1.74.0-14+b1 libboost-serialization1.74-dev=1.74.0-14+b1 libboost-serialization1.74.0=1.74.0-14+b1 libboost-test1.74-dev=1.74.0-14+b1 libboost-test1.74.0=1.74.0-14+b1 libboost1.74-dev=1.74.0-14+b1 libbrotli1=1.0.9-2+b3 libbsd0=0.11.6-1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcbor0.8=0.8.0-2 libcc1-0=12.1.0-2 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-4 libctf0=2.38-4 libcurl3-gnutls=7.83.1-1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.262 libdebhelper-perl=13.7.1 libdpkg-perl=1.21.7 libedit2=3.1-20210910-1 libelf1=0.187-1 libevent-2.1-7=2.1.12-stable-5+b1 libevent-core-2.1-7=2.1.12-stable-5+b1 libevent-dev=2.1.12-stable-5+b1 libevent-extra-2.1-7=2.1.12-stable-5+b1 libevent-openssl-2.1-7=2.1.12-stable-5+b1 libevent-pthreads-2.1-7=2.1.12-stable-5+b1 libfabric1=1.11.0-3 libffi8=3.4.2-4 libfido2-1=1.11.0-1+b1 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.3.0-1 libgcc-s1=12.1.0-2 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran-11-dev=11.3.0-1 libgfortran5=12.1.0-2 libglib2.0-0=2.72.1-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.4-2 libgomp1=12.1.0-2 libgpg-error0=1.45-2 libgssapi-krb5-2=1.19.2-2+b1 libhogweed6=3.7.3-1 libhtml-parser-perl=3.78-1 libhtml-tagset-perl=3.20-4 libhwloc-dev=2.7.1-1 libhwloc-plugins=2.7.1-1 libhwloc15=2.7.1-1 libibverbs-dev=39.0-1+b1 libibverbs1=39.0-1+b1 libicu-dev=71.1-3 libicu71=71.1-3 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=12.1.0-2 libjs-jquery=3.6.0+dfsg+~3.5.13-1 libjs-jquery-ui=1.13.1+dfsg-1 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 libldap-2.5-0=2.5.12+dfsg-1 liblocale-gettext-perl=1.07-4+b2 liblsan0=12.1.0-2 libltdl-dev=2.4.7-4 libltdl7=2.4.7-4 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-4 libmagic1=1:5.41-4 libmd0=1.0.4-1 libmount1=2.38-4 libmpc3=1.2.1-2 libmpfr6=4.1.0-3 libnettle8=3.7.3-1 libnghttp2-14=1.47.0-1 libnl-3-200=3.5.0-0.1 libnl-3-dev=3.5.0-0.1 libnl-route-3-200=3.5.0-0.1 libnl-route-3-dev=3.5.0-0.1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.14-3 libnuma1=2.0.14-3 libopenmpi-dev=4.1.3-2 libopenmpi3=4.1.3-2 libp11-kit0=0.24.1-1 libpam-modules=1.4.0-13 libpam-modules-bin=1.4.0-13 libpam-runtime=1.4.0-13 libpam0g=1.4.0-13 libpciaccess0=0.16-3 libpcre2-8-0=10.40-1 libpcre3=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.6-1 libpmix-dev=4.1.2-2 libpmix2=4.1.2-2 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libquadmath0=12.1.0-2 librdmacm1=39.0-1+b1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-4+b1 libsasl2-modules-db=2.1.28+dfsg-4+b1 libseccomp2=2.5.4-1 libselinux1=3.3-1+b2 libsemanage-common=3.3-1 libsemanage2=3.3-1+b2 libsepol2=3.3-1 libsigsegv2=2.14-1 libsmartcols1=2.38-4 libsparsehash-dev=2.0.3-2 libsqlite3-0=3.38.5-1 libsqlite3-dev=3.38.5-1 libssh2-1=1.10.0-3 libssl1.1=1.1.1o-1 libssl3=3.0.3-2 libstdc++-11-dev=11.3.0-1 libstdc++6=12.1.0-2 libsub-override-perl=0.09-2 libsystemd0=250.4-1 libtasn1-6=4.18.0-4 libtext-markdown-perl=1.000031-3 libtext-multimarkdown-perl=1.000035-2 libtinfo6=6.3+20220423-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-4 libtsan0=11.3.0-1 libubsan1=12.1.0-2 libuchardet0=0.0.7-1 libucx0=1.12.1-1 libudev1=250.4-1 libunistring2=1.0-1 liburi-perl=5.10-1 libuuid1=2.38-4 libx11-6=2:1.7.5-1 libx11-data=2:1.7.5-1 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxml2=2.9.14+dfsg-1 libxnvctrl0=470.103.01-2 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.17.3-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 ncurses-base=6.3+20220423-2 ncurses-bin=6.3+20220423-2 ocl-icd-libopencl1=2.2.14-3 openmpi-bin=4.1.3-2 openmpi-common=4.1.3-2 openssh-client=1:9.0p1-1 passwd=1:4.11.1+dfsg1-2 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.03-1 tar=1.34+dfsg-1 util-linux=2.38-4 util-linux-extra=2.38-4 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --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/20220517T034618Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220517T034618Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220514T161632Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220511T204932Z/ 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=2.3.5+dfsg-1 && mkdir -p /build/abyss-12IxkW && dpkg-source --no-check -x /*.dsc /build/abyss-12IxkW/abyss-2.3.5+dfsg && chown -R builduser:builduser /build/abyss-12IxkW" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/abyss-12IxkW/abyss-2.3.5+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652530776" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/abyss-12IxkW /tmp/abyss-2.3.5+dfsg-1nitusb7w bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.SIp9edetNZ 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.SIp9edetNZ Reading package lists... Building dependency tree... util-linux is already the newest version (2.38-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (1020 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 ... 4628 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.28-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.28-1_amd64.deb ... Unpacking fakeroot (1.28-1) ... Setting up libfakeroot:amd64 (1.28-1) ... Setting up fakeroot (1.28-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220517T034618Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220517T034618Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220514T161632Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220511T204932Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.SIp9edetNZ Get:1 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm InRelease [130 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220514T161632Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220511T204932Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main Sources [11.9 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main amd64 Packages [11.4 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220514T161632Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220514T161632Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220514T161632Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220514T161632Z unstable/main amd64 Packages [12.4 MB] Fetched 36.1 MB in 30s (1216 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.SIp9edetNZ I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d abyss=2.3.5+dfsg-1 && mkdir -p /build/abyss-12IxkW && dpkg-source --no-check -x /*.dsc /build/abyss-12IxkW/abyss-2.3.5+dfsg && chown -R builduser:builduser /build/abyss-12IxkW"' exec /tmp/mmdebstrap.SIp9edetNZ 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 3015 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main abyss 2.3.5+dfsg-1 (dsc) [2405 B] Get:2 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main abyss 2.3.5+dfsg-1 (tar) [1515 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220517T034618Z bookworm/main abyss 2.3.5+dfsg-1 (diff) [1498 kB] Fetched 3015 kB in 2s (1245 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'abyss_2.3.5+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting abyss in /build/abyss-12IxkW/abyss-2.3.5+dfsg dpkg-source: info: unpacking abyss_2.3.5+dfsg.orig.tar.xz dpkg-source: info: unpacking abyss_2.3.5+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying abyss-pe.patch dpkg-source: info: applying fix-privacy-breach.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/abyss-12IxkW/abyss-2.3.5+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1652530776" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.SIp9edetNZ dpkg-buildpackage: info: source package abyss dpkg-buildpackage: info: source version 2.3.5+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary-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:80: installing './config.guess' configure.ac:80: installing './config.sub' configure.ac:10: installing './install-sh' configure.ac:10: installing './missing' ABYSS/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' dh_auto_configure -- \ --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-mpi=/usr/lib/x86_64-linux-gnu/openmpi checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether g++ supports C++11 features with -std=c++11... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking whether UID '1000' is supported by ustar format... yes checking whether GID '1000' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking dependency style of g++ -std=c++11... none checking for gawk... (cached) mawk checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=c++11 accepts -g... (cached) yes checking for g++ -std=c++11 option to enable C++11 features... (cached) none needed checking for ranlib... ranlib checking for ghc... no ./configure: line 7029: : command not found checking for pandoc... no checking for ar... ar checking the archiver (ar) interface... ar checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for vfork.h... no checking for dlfcn.h... yes checking for fcntl.h... yes checking for float.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for sys/param.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for inline... inline checking for ptrdiff_t... yes checking for mode_t... yes checking for pid_t... yes checking for size_t... yes checking for ssize_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for std::hash... yes checking for std::tr1::hash... yes checking for std::tr1::tuple... yes checking for dup2... yes checking for gethostname... yes checking for getopt_long... yes checking for getpagesize... yes checking for memset... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking for fork... yes checking for vfork... yes checking for vprintf... yes checking for working fork... yes checking for working vfork... (cached) yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for GNU libc compatible malloc... yes checking for working memcmp... yes checking for GNU libc compatible realloc... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether HOST_NAME_MAX is declared... yes checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... 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 for mpi.h... yes checking for MPI_Init in -lmpi... yes checking for sqrt in -lm... yes checking for pow... yes checking for sqrt... yes checking for ceilf... yes checking for dlsym in -ldl... yes checking for functional... yes checking for tr1/functional... yes checking for boost/functional/hash.hpp... yes checking for boost/property_map/property_map.hpp... yes checking for google/sparse_hash_map... yes checking for unordered_map... yes checking for tr1/unordered_map... yes checking for unordered_set... yes checking for tr1/unordered_set... yes checking for boost/unordered_set.hpp... yes checking for sqlite3.h... yes checking for main in -lsqlite3... yes checking for g++ -std=c++11 option to support OpenMP... -fopenmp checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ABYSS/Makefile config.status: creating Align/Makefile config.status: creating Assembly/Makefile config.status: creating Common/Makefile config.status: creating DataLayer/Makefile config.status: creating FMIndex/Makefile config.status: creating Graph/Makefile config.status: creating Parallel/Makefile config.status: creating bin/Makefile config.status: creating doc/Makefile config.status: creating dialign/Makefile config.status: creating kmerprint/Makefile config.status: creating AdjList/Makefile config.status: creating Konnector/Makefile config.status: creating DAssembler/Makefile config.status: creating DistanceEst/Makefile config.status: creating Layout/Makefile config.status: creating Map/Makefile config.status: creating Overlap/Makefile config.status: creating PopBubbles/Makefile config.status: creating Scaffold/Makefile config.status: creating SimpleGraph/Makefile config.status: creating MergePaths/Makefile config.status: creating KAligner/Makefile config.status: creating PairedDBG/Makefile config.status: creating ParseAligns/Makefile config.status: creating PathOverlap/Makefile config.status: creating Consensus/Makefile config.status: creating FilterGraph/Makefile config.status: creating GapFiller/Makefile config.status: creating Sealer/Makefile config.status: creating vendor/gtest-1.7.0/Makefile config.status: creating RResolver/Makefile config.status: creating Unittest/Makefile config.status: creating LogKmerCount/Makefile config.status: creating Bloom/Makefile config.status: creating BloomDBG/Makefile config.status: creating DataBase/Makefile config.status: creating vendor/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' dh_auto_build make -j10 make[2]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' make all-recursive make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' Making all in bin make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/bin' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/bin' Making all in doc make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/doc' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/doc' Making all in Common make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Common' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libcommon_a-city.o `test -f 'city.cc' || echo './'`city.cc rm -f libcommon.a ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o libcommon_a-city.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcommon.a make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Common' Making all in Graph make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Graph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L. -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-todot abyss_todot-todot.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Graph' Making all in DataLayer make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataLayer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc rm -f libdatalayer.a ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdatalayer.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataLayer' Making all in DataBase make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataBase' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc rm -f libdb.a ar cru libdb.a libdb_a-DB.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdb.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataBase' Making all in FMIndex make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FMIndex' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc rm -f libfmindex.a ar cru libfmindex.a libfmindex_a-bit_array.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfmindex.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FMIndex' Making all in Assembly make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Assembly' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cc' || echo './'`AssemblyAlgorithms.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libassembly_a-Options.o `test -f 'Options.cc' || echo './'`Options.cc rm -f libassembly.a ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-Options.o ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libassembly.a make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Assembly' Making all in dialign make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/dialign' gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o museq.o museq.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alig.o alig.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diag.o diag.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o io.o io.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o orf.o orf.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o prob.o prob.c gcc -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o translate.o translate.c assemble.c:40:20: warning: inline function ‘align_diag’ declared but never defined 40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); | ^~~~~~~~~~ assemble.c:37:32: warning: inline function ‘find_eqc’ declared but never defined 37 | extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); | ^~~~~~~~ assemble.c:25:39: warning: inline function ‘find_diags_guided’ declared but never defined 25 | extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix, | ^~~~~~~~~~~~~~~~~ assemble.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ assemble.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ alig.c:15:20: warning: inline function ‘calc_ov_weight’ declared but never defined 15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, | ^~~~~~~~~~~~~~ alig.c:13:20: warning: inline function ‘calc_weight’ declared but never defined 13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, | ^~~~~~~~~~~ diag.c:1456:17: warning: ‘real_calc_weight’ is static but used in inline function ‘find_diags_dyn’ which is not static 1456 | real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn); | ^~~~~~~~~~~~~~~~ io.c: In function ‘read_scr_matrix’: io.c:270:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 270 | fscanf( fp, "%i", &is); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:282:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 282 | fscanf(fp, "%s\n", rline); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘read_diag_prob_dist’: io.c:371:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 371 | fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libdialign.a ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libdialign.a gcc -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o dialign museq.o libdialign.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/dialign' Making all in Align make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Align' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo './'`mergepairs.cc rm -f libalign.a ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libalign.a g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Align' Making all in ABYSS make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ABYSS' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ABYSS' Making all in Parallel make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Parallel' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -DPAIRED_DBG -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -lmpi -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Parallel' Making all in Bloom make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Bloom' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom-bloom.o `test -f 'bloom.cc' || echo './'`bloom.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom abyss_bloom-bloom.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Bloom' Making all in BloomDBG make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/BloomDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../vendor -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_bloom_dbg-bloom-dbg.o `test -f 'bloom-dbg.cc' || echo './'`bloom-dbg.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-bloom-dbg abyss_bloom_dbg-bloom-dbg.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/BloomDBG' Making all in Konnector make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Konnector' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o konnector-konnector.o `test -f 'konnector.cc' || echo './'`konnector.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Konnector' Making all in Consensus make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Consensus' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Consensus' Making all in DAssembler make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DAssembler' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DAssembler' Making all in DistanceEst make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DistanceEst' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DistanceEst' Making all in KAligner make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/KAligner' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/KAligner' Making all in Layout make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Layout' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Layout' Making all in LogKmerCount make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/LogKmerCount' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/LogKmerCount' Making all in Map make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Map' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Map' Making all in MergePaths make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/MergePaths' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/MergePaths' Making all in Overlap make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Overlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Overlap' Making all in PairedDBG make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PairedDBG' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o KmerPair.o KmerPair.cc rm -f libpaireddbg.a ar cru libpaireddbg.a KmerPair.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpaireddbg.a g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PairedDBG' Making all in ParseAligns make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ParseAligns' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ParseAligns' Making all in PathOverlap make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PathOverlap' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PathOverlap' Making all in PopBubbles make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PopBubbles' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PopBubbles' Making all in Scaffold make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Scaffold' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Scaffold' Making all in SimpleGraph make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/SimpleGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp g++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/SimpleGraph' Making all in kmerprint make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/kmerprint' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/kmerprint' Making all in FilterGraph make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FilterGraph' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FilterGraph' Making all in GapFiller make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/GapFiller' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/GapFiller' Making all in Sealer make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Sealer' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Sealer' Making all in RResolver make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/RResolver' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_rresolver_short-RResolverShort.o `test -f 'RResolverShort.cpp' || echo './'`RResolverShort.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-RAlgorithmsShort.o `test -f 'RAlgorithmsShort.cpp' || echo './'`RAlgorithmsShort.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-BloomFilters.o `test -f 'BloomFilters.cpp' || echo './'`BloomFilters.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-SequenceTree.o `test -f 'SequenceTree.cpp' || echo './'`SequenceTree.cpp g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o libralgorithmsshort_a-RUtils.o `test -f 'RUtils.cpp' || echo './'`RUtils.cpp rm -f libralgorithmsshort.a ar cru libralgorithmsshort.a libralgorithmsshort_a-RAlgorithmsShort.o libralgorithmsshort_a-BloomFilters.o libralgorithmsshort_a-Contigs.o libralgorithmsshort_a-SequenceTree.o libralgorithmsshort_a-RUtils.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libralgorithmsshort.a g++ -std=c++11 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -pthread -o abyss-rresolver-short abyss_rresolver_short-RResolverShort.o abyss_rresolver_short-Contigs.o ../DataLayer/libdatalayer.a ../Common/libcommon.a libralgorithmsshort.a -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/RResolver' Making all in AdjList make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/AdjList' g++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -DPAIRED_DBG -I/build/abyss-12IxkW/abyss-2.3.5+dfsg -isystem/usr/lib/x86_64-linux-gnu/openmpi/include -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/abyss-12IxkW/abyss-2.3.5+dfsg/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/abyss-12IxkW/abyss-2.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -L/usr/lib/x86_64-linux-gnu/openmpi/lib -Wl,-z,relro -Wl,-z,now -o AdjList AdjList-AdjList.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../PairedDBG/libpaireddbg.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/AdjList' Making all in vendor make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor' Making all in vendor/gtest-1.7.0 make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' Making all in Unittest make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Unittest' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' make[2]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' markdown README.md > README.html make[1]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' dh_auto_install --destdir=debian/tmp make -j10 install DESTDIR=/build/abyss-12IxkW/abyss-2.3.5\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' Making install in bin make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/bin' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/bin' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+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-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/bin' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/bin' Making install in doc make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/doc' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/doc' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 flowchart.pdf flowchart_simplified.pdf '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/doc' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/doc' Making install in Common make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Common' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Common' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Common' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Common' Making install in Graph make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Graph' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Graph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-gc abyss-todot '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Graph' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Graph' Making install in DataLayer make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataLayer' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataLayer' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-fac abyss-tofastq '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataLayer' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataLayer' Making install in DataBase make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataBase' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataBase' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-csv '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-db-txt '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataBase' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DataBase' Making install in FMIndex make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FMIndex' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FMIndex' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FMIndex' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FMIndex' Making install in Assembly make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Assembly' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Assembly' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Assembly' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Assembly' Making install in dialign make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/dialign' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/dialign' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/dialign' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/dialign' Making install in Align make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Align' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Align' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-align abyss-mergepairs '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Align' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Align' Making install in ABYSS make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ABYSS' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ABYSS' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c ABYSS '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ABYSS' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ABYSS' Making install in Parallel make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Parallel' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Parallel' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c ABYSS-P abyss-paired-dbg-mpi '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Parallel' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Parallel' Making install in Bloom make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Bloom' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Bloom' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Bloom' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Bloom' Making install in BloomDBG make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/BloomDBG' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/BloomDBG' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-bloom-dbg '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/BloomDBG' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/BloomDBG' Making install in Konnector make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Konnector' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Konnector' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c konnector '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Konnector' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Konnector' Making install in Consensus make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Consensus' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Consensus' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c Consensus '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Consensus' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Consensus' Making install in DAssembler make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DAssembler' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DAssembler' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c DAssembler '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DAssembler' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DAssembler' Making install in DistanceEst make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DistanceEst' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DistanceEst' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c DistanceEst DistanceEst-ssq '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DistanceEst' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/DistanceEst' Making install in KAligner make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/KAligner' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/KAligner' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c KAligner '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/KAligner' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/KAligner' Making install in Layout make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Layout' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Layout' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-layout '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Layout' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Layout' Making install in LogKmerCount make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/LogKmerCount' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/LogKmerCount' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c logcounter '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/LogKmerCount' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/LogKmerCount' Making install in Map make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Map' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Map' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-index abyss-map abyss-map-ssq abyss-overlap '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Map' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Map' Making install in MergePaths make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/MergePaths' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/MergePaths' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c MergePaths MergeContigs PathConsensus '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/MergePaths' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/MergePaths' Making install in Overlap make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Overlap' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Overlap' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c Overlap '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Overlap' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Overlap' Making install in PairedDBG make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PairedDBG' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PairedDBG' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-paired-dbg '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PairedDBG' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PairedDBG' Making install in ParseAligns make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ParseAligns' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ParseAligns' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-fixmate abyss-fixmate-ssq ParseAligns '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ParseAligns' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/ParseAligns' Making install in PathOverlap make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PathOverlap' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PathOverlap' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c PathOverlap '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PathOverlap' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PathOverlap' Making install in PopBubbles make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PopBubbles' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PopBubbles' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c PopBubbles '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PopBubbles' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/PopBubbles' Making install in Scaffold make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Scaffold' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Scaffold' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-scaffold abyss-junction abyss-longseqdist '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Scaffold' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Scaffold' Making install in SimpleGraph make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/SimpleGraph' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/SimpleGraph' make[4]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c SimpleGraph '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/SimpleGraph' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/SimpleGraph' Making install in kmerprint make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/kmerprint' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/kmerprint' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/kmerprint' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/kmerprint' Making install in FilterGraph make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FilterGraph' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FilterGraph' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-filtergraph '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FilterGraph' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/FilterGraph' Making install in GapFiller make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/GapFiller' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/GapFiller' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-gapfill '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/GapFiller' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/GapFiller' Making install in Sealer make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Sealer' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Sealer' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' /usr/bin/install -c abyss-sealer '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Sealer' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Sealer' Making install in RResolver make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/RResolver' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/RResolver' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c abyss-rresolver-short '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/RResolver' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/RResolver' Making install in AdjList make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/AdjList' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/AdjList' /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c AdjList '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/bin' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/AdjList' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/AdjList' Making install in vendor make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor' Making install in vendor/gtest-1.7.0 make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/vendor/gtest-1.7.0' Making install in Unittest make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Unittest' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Unittest' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Unittest' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg/Unittest' make[3]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' make[4]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' /usr/bin/install -c -m 644 ChangeLog CITATION.bib CITATION.md COPYRIGHT LICENSE README.md '/build/abyss-12IxkW/abyss-2.3.5+dfsg/debian/tmp/usr/share/doc/abyss' make[4]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' make[3]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' make[2]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' mkdir -p debian/tmp/usr/share/man/man1 PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/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-12IxkW/abyss-2.3.5+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/abyss-12IxkW/abyss-2.3.5+dfsg' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/abyss-12IxkW/abyss-2.3.5+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 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'abyss-dbgsym' in '../abyss-dbgsym_2.3.5+dfsg-1_amd64.deb'. dpkg-deb: building package 'abyss' in '../abyss_2.3.5+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../abyss_2.3.5+dfsg-1_amd64.buildinfo dpkg-genchanges --build=any -O../abyss_2.3.5+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-12IxkW /tmp/abyss-2.3.5+dfsg-1nitusb7w I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.SIp9edetNZ... I: success in 872.7015 seconds md5: abyss-dbgsym_2.3.5+dfsg-1_amd64.deb: OK md5: abyss_2.3.5+dfsg-1_amd64.deb: OK sha1: abyss-dbgsym_2.3.5+dfsg-1_amd64.deb: OK sha1: abyss_2.3.5+dfsg-1_amd64.deb: OK sha256: abyss-dbgsym_2.3.5+dfsg-1_amd64.deb: OK sha256: abyss_2.3.5+dfsg-1_amd64.deb: OK Checksums: OK