RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lcy01-32 4.4.0-77-generic #98-Ubuntu SMP Wed Apr 26 08:34:02 UTC 2017 x86_64 Buildd toolchain package versions: launchpad-buildd_142 python-lpbuildd_142 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1 dpkg-dev_1.18.4ubuntu1.2 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.11. Syncing the system clock with the buildd NTP service... 12 May 10:58:40 ntpdate[1804]: adjust time server 10.211.37.1 offset -0.001413 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12573691', '/home/buildd/filecache-default/7fe38ae672de2c40a7e6ba74a0e6690544a5bb48'] Unpacking chroot for build PACKAGEBUILD-12573691 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12573691'] Mounting chroot for build PACKAGEBUILD-12573691 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12573691', 'deb http://ppa.launchpad.net/bhavi/ppa4/ubuntu artful main', 'deb http://ftpmaster.internal/ubuntu artful main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu artful-updates main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-12573691 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12573691', 'i386'] Updating debian chroot for build PACKAGEBUILD-12573691 Get:1 http://ftpmaster.internal/ubuntu artful InRelease [237 kB] Get:2 http://ftpmaster.internal/ubuntu artful-security InRelease [65.5 kB] Get:3 http://ftpmaster.internal/ubuntu artful-updates InRelease [65.5 kB] Get:4 http://ppa.launchpad.net/bhavi/ppa4/ubuntu artful InRelease [15.4 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main i386 Packages [1164 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [564 kB] Get:7 http://ftpmaster.internal/ubuntu artful/restricted i386 Packages [8640 B] Get:8 http://ftpmaster.internal/ubuntu artful/restricted Translation-en [2724 B] Get:9 http://ftpmaster.internal/ubuntu artful/universe i386 Packages [8241 kB] Ign:4 http://ppa.launchpad.net/bhavi/ppa4/ubuntu artful InRelease Get:10 http://ppa.launchpad.net/bhavi/ppa4/ubuntu artful/main i386 Packages [888 B] Get:11 http://ppa.launchpad.net/bhavi/ppa4/ubuntu artful/main Translation-en [444 B] Get:12 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4747 kB] Get:13 http://ftpmaster.internal/ubuntu artful/multiverse i386 Packages [148 kB] Get:14 http://ftpmaster.internal/ubuntu artful/multiverse Translation-en [110 kB] Fetched 15.4 MB in 4s (3340 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net/bhavi/ppa4/ubuntu artful InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY D90C3C3D0A3A05EF W: The repository 'http://ppa.launchpad.net/bhavi/ppa4/ubuntu artful InRelease' is not signed. Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-7-base The following packages will be upgraded: apt apt-transport-https cpp-6 debianutils dmsetup dpkg dpkg-dev g++-6 gcc-6 gcc-6-base libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libatomic1 libcc1-0 libcilkrts5 libdevmapper1.02.1 libdpkg-perl libgcc-6-dev libgcc1 libgnutls30 libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libitm1 libkmod2 libkrb5-26-heimdal libmpx2 libquadmath0 libroken18-heimdal libstdc++-6-dev libstdc++6 libsystemd0 libubsan0 libudev1 libusb-0.1-4 libwind0-heimdal systemd systemd-sysv 43 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 35.8 MB of archives. After this operation, 306 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main i386 debianutils i386 4.8.1.1 [85.7 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main i386 dpkg i386 1.18.23ubuntu6 [1158 kB] Get:3 http://ftpmaster.internal/ubuntu artful/main i386 gcc-7-base i386 7.1.0-4ubuntu1 [18.4 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main i386 libgcc1 i386 1:7.1.0-4ubuntu1 [46.9 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main i386 libstdc++6 i386 7.1.0-4ubuntu1 [436 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main i386 libapt-pkg5.0 i386 1.4.2 [857 kB] Get:7 http://ftpmaster.internal/ubuntu artful/main i386 apt i386 1.4.2 [1130 kB] Get:8 http://ftpmaster.internal/ubuntu artful/main i386 libapparmor1 i386 2.11.0-2ubuntu5 [31.6 kB] Get:9 http://ftpmaster.internal/ubuntu artful/main i386 libkmod2 i386 24-1ubuntu1 [46.0 kB] Get:10 http://ftpmaster.internal/ubuntu artful/main i386 systemd i386 233-6ubuntu1 [2475 kB] Get:11 http://ftpmaster.internal/ubuntu artful/main i386 libsystemd0 i386 233-6ubuntu1 [230 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main i386 systemd-sysv i386 233-6ubuntu1 [13.6 kB] Get:13 http://ftpmaster.internal/ubuntu artful/main i386 libudev1 i386 233-6ubuntu1 [61.1 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main i386 libdevmapper1.02.1 i386 2:1.02.137-2ubuntu1 [146 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main i386 dmsetup i386 2:1.02.137-2ubuntu1 [72.9 kB] Get:16 http://ftpmaster.internal/ubuntu artful/main i386 libroken18-heimdal i386 7.1.0+dfsg-13 [44.4 kB] Get:17 http://ftpmaster.internal/ubuntu artful/main i386 libasn1-8-heimdal i386 7.1.0+dfsg-13 [187 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main i386 libgnutls30 i386 3.5.8-5ubuntu1 [693 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main i386 libheimbase1-heimdal i386 7.1.0+dfsg-13 [31.9 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main i386 libhcrypto4-heimdal i386 7.1.0+dfsg-13 [93.4 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main i386 libwind0-heimdal i386 7.1.0+dfsg-13 [48.6 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main i386 libhx509-5-heimdal i386 7.1.0+dfsg-13 [118 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main i386 libkrb5-26-heimdal i386 7.1.0+dfsg-13 [232 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main i386 libheimntlm0-heimdal i386 7.1.0+dfsg-13 [16.6 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main i386 libgssapi3-heimdal i386 7.1.0+dfsg-13 [108 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main i386 apt-transport-https i386 1.4.2 [38.3 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main i386 libquadmath0 i386 7.1.0-4ubuntu1 [204 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main i386 libitm1 i386 7.1.0-4ubuntu1 [30.3 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main i386 libmpx2 i386 7.1.0-4ubuntu1 [13.0 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main i386 libubsan0 i386 7.1.0-4ubuntu1 [134 kB] Get:31 http://ftpmaster.internal/ubuntu artful/main i386 libcilkrts5 i386 7.1.0-4ubuntu1 [47.3 kB] Get:32 http://ftpmaster.internal/ubuntu artful/main i386 libgomp1 i386 7.1.0-4ubuntu1 [80.2 kB] Get:33 http://ftpmaster.internal/ubuntu artful/main i386 libatomic1 i386 7.1.0-4ubuntu1 [9696 B] Get:34 http://ftpmaster.internal/ubuntu artful/main i386 libasan3 i386 6.3.0-17ubuntu1 [308 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main i386 g++-6 i386 6.3.0-17ubuntu1 [7633 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main i386 libstdc++-6-dev i386 6.3.0-17ubuntu1 [1452 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main i386 gcc-6 i386 6.3.0-17ubuntu1 [7436 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main i386 libgcc-6-dev i386 6.3.0-17ubuntu1 [2309 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main i386 libcc1-0 i386 7.1.0-4ubuntu1 [41.3 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main i386 cpp-6 i386 6.3.0-17ubuntu1 [6831 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main i386 gcc-6-base i386 6.3.0-17ubuntu1 [17.1 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main i386 dpkg-dev all 1.18.23ubuntu6 [607 kB] Get:43 http://ftpmaster.internal/ubuntu artful/main i386 libdpkg-perl all 1.18.23ubuntu6 [209 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main i386 libusb-0.1-4 i386 2:0.1.12-31 [17.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 35.8 MB in 1s (18.6 MB/s) (Reading database ... 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Setting up libgssapi3-heimdal:i386 (7.1.0+dfsg-13) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12573691', 'i386', 'artful', '-c', 'chroot:autobuild', '--arch=i386', '--dist=artful', '--purge=never', '--nolog', 'consensuscore_1.0.2-2build1.dsc'] Initiating build PACKAGEBUILD-12573691 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-77-generic #98-Ubuntu SMP Wed Apr 26 08:34:02 UTC 2017 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-32.buildd +==============================================================================+ | consensuscore 1.0.2-2build1 (i386) 12 May 2017 10:59 | +==============================================================================+ Package: consensuscore Version: 1.0.2-2build1 Source Version: 1.0.2-2build1 Distribution: artful Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/consensuscore-J40cok/consensuscore-1.0.2' with '<>' I: NOTICE: Log filtering will replace 'build/consensuscore-J40cok' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12573691/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- consensuscore_1.0.2-2build1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-LDXhDP/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-LDXhDP/apt_archive ./ InRelease Get:2 copy:/<>/resolver-LDXhDP/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-LDXhDP/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-LDXhDP/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-LDXhDP/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (222 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 776 B of archives. After this operation, 0 B of additional disk space will be used. 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Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 9), dh-python, dh-exec, libboost-dev, swig, python-setuptools, python-all-dev, python-numpy, python3-setuptools, python3-all-dev, python3-numpy Filtered Build-Depends: debhelper (>= 9), dh-python, dh-exec, libboost-dev, swig, python-setuptools, python-all-dev, python-numpy, python3-setuptools, python3-all-dev, python3-numpy dpkg-deb: building package 'sbuild-build-depends-consensuscore-dummy' in '/<>/resolver-gfuiE9/apt_archive/sbuild-build-depends-consensuscore-dummy.deb'. Ign:1 copy:/<>/resolver-gfuiE9/apt_archive ./ InRelease Get:2 copy:/<>/resolver-gfuiE9/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-gfuiE9/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-gfuiE9/apt_archive ./ Sources [270 B] Get:5 copy:/<>/resolver-gfuiE9/apt_archive ./ Packages [591 B] Fetched 2980 B in 0s (248 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install consensuscore build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas-common libblas3 libboost-dev libboost1.62-dev libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libicu57 liblapack3 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-numpy python-pkg-resources python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-numpy python3-pkg-resources python3-setuptools python3.5 python3.5-dev python3.5-minimal swig swig3.0 Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.62-doc libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev libboost-filesystem1.62-dev libboost-graph1.62-dev libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-program-options1.62-dev libboost-python1.62-dev libboost-random1.62-dev libboost-regex1.62-dev libboost-serialization1.62-dev libboost-signals1.62-dev libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less www-browser libmail-box-perl python-doc python-tk gfortran python-nose python-numpy-dbg python-numpy-doc python-setuptools-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3-nose python3-numpy-dbg python3.5-venv python3.5-doc swig-doc swig-examples swig3.0-examples swig3.0-doc Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following packages will be REMOVED: pkg-create-dbgsym* The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas-common libblas3 libboost-dev libboost1.62-dev libbsd0 libcroco3 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libicu57 liblapack3 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.5 libpython3.5-dev libpython3.5-minimal libpython3.5-stdlib libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-minimal python-numpy python-pkg-resources python-setuptools python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-minimal python3-numpy python3-pkg-resources python3-setuptools python3.5 python3.5-dev python3.5-minimal sbuild-build-depends-consensuscore-dummy swig swig3.0 0 upgraded, 80 newly installed, 1 to remove and 0 not upgraded. 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Setting up libblas3 (3.7.0-1) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Processing triggers for libc-bin (2.24-9ubuntu2) ... Setting up autotools-dev (20161112.1) ... Setting up libexpat1-dev:i386 (2.2.0-2) ... Setting up libboost-dev:i386 (1.62.0.1) ... Setting up bsdmainutils (9.0.12ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpython2.7-stdlib:i386 (2.7.13-2) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up libmpdec2:i386 (2.4.2-1) ... Setting up libfile-stripnondeterminism-perl (0.033-2) ... Setting up swig (3.0.10-1.1) ... Setting up gettext (0.19.8.1-2ubuntu1) ... Setting up liblapack3 (3.7.0-1) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libpython3.5-stdlib:i386 (3.5.3-1) ... Setting up python2.7 (2.7.13-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.29-3) ... Setting up libpython-stdlib:i386 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libpython2.7:i386 (2.7.13-2) ... Setting up automake (1:1.15-5ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2.7-dev:i386 (2.7.13-2) ... Setting up python2.7-dev (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up python3.5 (3.5.3-1) ... Setting up libpython3-stdlib:i386 (3.5.3-1) ... Setting up libpython-dev:i386 (2.7.13-2) ... Setting up po-debconf (1.0.20) ... Setting up libpython3.5:i386 (3.5.3-1) ... Setting up python-dev (2.7.13-2) ... Setting up libpython-all-dev:i386 (2.7.13-2) ... Setting up python-pkg-resources (33.1.1-1) ... Setting up libpython3.5-dev:i386 (3.5.3-1) ... Setting up python-numpy (1:1.12.1-1ubuntu1) ... Setting up python3.5-dev (3.5.3-1) ... Setting up python-all (2.7.13-2) ... Setting up libpython3-dev:i386 (3.5.3-1) ... Setting up python-setuptools (33.1.1-1) ... Setting up python-all-dev (2.7.13-2) ... Setting up libpython3-all-dev:i386 (3.5.3-1) ... Setting up dh-autoreconf (14) ... Setting up python3 (3.5.3-1) ... Setting up python3-numpy (1:1.12.1-1ubuntu1) ... Setting up python3-dev (3.5.3-1) ... Setting up python3-pkg-resources (33.1.1-1) ... Setting up dh-strip-nondeterminism (0.033-2) ... Setting up python3-all (3.5.3-1) ... Setting up python3-setuptools (33.1.1-1) ... Setting up dh-python (2.20170125) ... Setting up debhelper (10.2.5ubuntu2) ... Setting up python3-all-dev (3.5.3-1) ... Setting up dh-exec (0.23build1) ... Setting up sbuild-build-depends-consensuscore-dummy (0.invalid.0) ... (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 ... 31496 files and directories currently installed.) Purging configuration files for pkg-create-dbgsym (0.73) ... Processing triggers for libc-bin (2.24-9ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-77-generic amd64 (i686) Toolchain package versions: binutils_2.28-4ubuntu1 dpkg-dev_1.18.23ubuntu6 g++-6_6.3.0-17ubuntu1 gcc-6_6.3.0-17ubuntu1 libc6-dev_2.24-9ubuntu2 libstdc++-6-dev_6.3.0-17ubuntu1 libstdc++6_7.1.0-4ubuntu1 linux-libc-dev_4.10.0-20.22 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.20-1 apt_1.4.2 apt-transport-https_1.4.2 autoconf_2.69-10 automake_1:1.15-5ubuntu1 autopoint_0.19.8.1-2ubuntu1 autotools-dev_20161112.1 base-files_9.6ubuntu99 base-passwd_3.5.43 bash_4.4-2ubuntu1 binutils_2.28-4ubuntu1 bsdmainutils_9.0.12ubuntu1 bsdutils_1:2.29-1ubuntu2 build-essential_12.1ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20161130 coreutils_8.26-3ubuntu3 cpp_4:6.3.0-2ubuntu1 cpp-6_6.3.0-17ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.60ubuntu1 debhelper_10.2.5ubuntu2 debianutils_4.8.1.1 dh-autoreconf_14 dh-exec_0.23build1 dh-python_2.20170125 dh-strip-nondeterminism_0.033-2 diffutils_1:3.5-3 dmsetup_2:1.02.137-2ubuntu1 dpkg_1.18.23ubuntu6 dpkg-dev_1.18.23ubuntu6 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-1ubuntu2 file_1:5.29-3 findutils_4.6.0+git+20161106-2 g++_4:6.3.0-2ubuntu1 g++-6_6.3.0-17ubuntu1 gcc_4:6.3.0-2ubuntu1 gcc-6_6.3.0-17ubuntu1 gcc-6-base_6.3.0-17ubuntu1 gcc-7-base_7.1.0-4ubuntu1 gettext_0.19.8.1-2ubuntu1 gettext-base_0.19.8.1-2ubuntu1 gnupg_2.1.15-1ubuntu7 gnupg-agent_2.1.15-1ubuntu7 gpgv_2.1.15-1ubuntu7 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5ubuntu1 hostname_3.18 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu5 libapt-pkg5.0_1.4.2 libarchive-zip-perl_1.59-1 libasan3_6.3.0-17ubuntu1 libasn1-8-heimdal_7.1.0+dfsg-13 libassuan0_2.4.3-2 libatomic1_7.1.0-4ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.6.6-1ubuntu1 libaudit1_1:2.6.6-1ubuntu1 libblas-common_3.7.0-1 libblas3_3.7.0-1 libblkid1_2.29-1ubuntu2 libboost-dev_1.62.0.1 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-9ubuntu2 libc-dev-bin_2.24-9ubuntu2 libc6_2.24-9ubuntu2 libc6-dev_2.24-9ubuntu2 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-4ubuntu1 libcilkrts5_7.1.0-4ubuntu1 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.52.1-5ubuntu1 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.137-2ubuntu1 libdpkg-perl_1.18.23ubuntu6 libexpat1_2.2.0-2 libexpat1-dev_2.2.0-2 libfakeroot_1.21-1ubuntu2 libfdisk1_2.29-1ubuntu2 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.033-2 libgcc-6-dev_6.3.0-17ubuntu1 libgcc1_1:7.1.0-4ubuntu1 libgcrypt20_1.7.6-1 libgdbm3_1.8.3-14 libgfortran3_6.3.0-17ubuntu1 libglib2.0-0_2.53.1-1 libgmp10_2:6.1.2+dfsg-1 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pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.13-2 python-all_2.7.13-2 python-all-dev_2.7.13-2 python-dev_2.7.13-2 python-minimal_2.7.13-2 python-numpy_1:1.12.1-1ubuntu1 python-pkg-resources_33.1.1-1 python-setuptools_33.1.1-1 python2.7_2.7.13-2 python2.7-dev_2.7.13-2 python2.7-minimal_2.7.13-2 python3_3.5.3-1 python3-all_3.5.3-1 python3-all-dev_3.5.3-1 python3-dev_3.5.3-1 python3-minimal_3.5.3-1 python3-numpy_1:1.12.1-1ubuntu1 python3-pkg-resources_33.1.1-1 python3-setuptools_33.1.1-1 python3.5_3.5.3-1 python3.5-dev_3.5.3-1 python3.5-minimal_3.5.3-1 readline-common_7.0-0ubuntu2 sbuild-build-depends-consensuscore-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 swig_3.0.10-1.1 swig3.0_3.0.10-1.1 systemd_233-6ubuntu1 systemd-sysv_233-6ubuntu1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1.1 tzdata_2017b-1 ubuntu-keyring_2016.10.27 util-linux_2.29-1ubuntu2 xz-utils_5.2.2-1.2 zlib1g_1:1.2.11.dfsg-0ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri May 12 10:56:09 2017 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./consensuscore_1.0.2-2build1.dsc dpkg-source: info: extracting consensuscore in consensuscore-1.0.2 dpkg-source: info: unpacking consensuscore_1.0.2.orig.tar.gz dpkg-source: info: unpacking consensuscore_1.0.2-2build1.debian.tar.xz dpkg-source: info: applying spelling.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying gcc-6.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.0.2-2build1 dpkg-buildpackage: info: source distribution artful dpkg-source --before-build consensuscore-1.0.2 dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --with python2,python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:184: python2.7 setup.py clean WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/<>/.pybuild/pythonX.Y_2.7/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:184: python3.5 setup.py clean WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/<>/.pybuild/pythonX.Y_3.5/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.5' does not exist -- can't clean it dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python2,python3 --buildsystem=pybuild dh_testdir -a -O--buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:184: python2.7 setup.py config WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config I: pybuild base:184: python3.5 setup.py config WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python setup.py build WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig3.0 PYTHON_INCLUDE = /usr/include/python2.7 NUMPY_INCLUDE = /usr/lib/python2.7/dist-packages/numpy/core/include DEBUG = CPP_ABI = c++98 make[1]: Entering directory '/<>' make -f make/Cpp.mk make[2]: Entering directory '/<>' mkdir -p /<>/build/C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Utils.cpp -o /<>/build/C++/Utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Utils.o -MM src/C++/Utils.cpp > /<>/build/C++/Utils.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Statistics/Binomial.cpp -o /<>/build/C++/Binomial.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /<>/build/C++/Binomial.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Logging/Logging.cpp -o /<>/build/C++/Logging.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /<>/build/C++/Logging.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Poa/PoaGraphImpl.cpp -o /<>/build/C++/PoaGraphImpl.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /<>/build/C++/PoaGraphImpl.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Poa/PoaGraph.cpp -o /<>/build/C++/PoaGraph.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /<>/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Poa/PoaGraphTraversals.cpp -o /<>/build/C++/PoaGraphTraversals.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /<>/build/C++/PoaGraphTraversals.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Poa/PoaConsensus.cpp -o /<>/build/C++/PoaConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /<>/build/C++/PoaConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Poa/RangeFinder.cpp -o /<>/build/C++/RangeFinder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /<>/build/C++/RangeFinder.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Version.cpp -o /<>/build/C++/Version.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Version.o -MM src/C++/Version.cpp > /<>/build/C++/Version.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Sequence.cpp -o /<>/build/C++/Sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /<>/build/C++/Sequence.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Mutation.cpp -o /<>/build/C++/Mutation.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /<>/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Quiver/ReadScorer.cpp -o /<>/build/C++/ReadScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /<>/build/C++/ReadScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /<>/build/C++/MultiReadMutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /<>/build/C++/MultiReadMutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Quiver/SimpleRecursor.cpp -o /<>/build/C++/SimpleRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /<>/build/C++/SimpleRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Quiver/QuiverConsensus.cpp -o /<>/build/C++/QuiverConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /<>/build/C++/QuiverConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Quiver/MutationEnumerator.cpp -o /<>/build/C++/MutationEnumerator.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /<>/build/C++/MutationEnumerator.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Quiver/MutationScorer.cpp -o /<>/build/C++/MutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /<>/build/C++/MutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Quiver/QuiverConfig.cpp -o /<>/build/C++/QuiverConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /<>/build/C++/QuiverConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Quiver/SseRecursor.cpp -o /<>/build/C++/SseRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /<>/build/C++/SseRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Quiver/Diploid.cpp -o /<>/build/C++/Diploid.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /<>/build/C++/Diploid.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Quiver/detail/RecursorBase.cpp -o /<>/build/C++/RecursorBase.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /<>/build/C++/RecursorBase.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Coverage.cpp -o /<>/build/C++/Coverage.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /<>/build/C++/Coverage.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Checksum.cpp -o /<>/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /<>/build/C++/Checksum.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Features.cpp -o /<>/build/C++/Features.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Features.o -MM src/C++/Features.cpp > /<>/build/C++/Features.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Feature.cpp -o /<>/build/C++/Feature.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Feature.o -MM src/C++/Feature.cpp > /<>/build/C++/Feature.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Matrix/DenseMatrix.cpp -o /<>/build/C++/DenseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /<>/build/C++/DenseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Matrix/SparseMatrix.cpp -o /<>/build/C++/SparseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /<>/build/C++/SparseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Edna/EdnaCounts.cpp -o /<>/build/C++/EdnaCounts.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /<>/build/C++/EdnaCounts.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Read.cpp -o /<>/build/C++/Read.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/Read.o -MM src/C++/Read.cpp > /<>/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Align/AffineAlignment.cpp -o /<>/build/C++/AffineAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /<>/build/C++/AffineAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Align/PairwiseAlignment.cpp -o /<>/build/C++/PairwiseAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /<>/build/C++/PairwiseAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Align/AlignConfig.cpp -o /<>/build/C++/AlignConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /<>/build/C++/AlignConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++98 -Wall -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -c src/C++/Align/LinearAlignment.cpp -o /<>/build/C++/LinearAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -MT /<>/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /<>/build/C++/LinearAlignment.d ar crs /<>/build/C++/libConsensusCore.a /<>/build/C++/Utils.o /<>/build/C++/Binomial.o /<>/build/C++/Logging.o /<>/build/C++/PoaGraphImpl.o /<>/build/C++/PoaGraph.o /<>/build/C++/PoaGraphTraversals.o /<>/build/C++/PoaConsensus.o /<>/build/C++/RangeFinder.o /<>/build/C++/Version.o /<>/build/C++/Sequence.o /<>/build/C++/Mutation.o /<>/build/C++/ReadScorer.o /<>/build/C++/MultiReadMutationScorer.o /<>/build/C++/SimpleRecursor.o /<>/build/C++/QuiverConsensus.o /<>/build/C++/MutationEnumerator.o /<>/build/C++/MutationScorer.o /<>/build/C++/QuiverConfig.o /<>/build/C++/SseRecursor.o /<>/build/C++/Diploid.o /<>/build/C++/RecursorBase.o /<>/build/C++/Coverage.o /<>/build/C++/Checksum.o /<>/build/C++/Features.o /<>/build/C++/Feature.o /<>/build/C++/DenseMatrix.o /<>/build/C++/SparseMatrix.o /<>/build/C++/EdnaCounts.o /<>/build/C++/Read.o /<>/build/C++/AffineAlignment.o /<>/build/C++/PairwiseAlignment.o /<>/build/C++/AlignConfig.o /<>/build/C++/LinearAlignment.o touch /<>/build/C++/libConsensusCore.a make[2]: Leaving directory '/<>' make -f make/Python.mk make[2]: Entering directory '/<>' mkdir -p /<>/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/<>/include -I/<>/external -module ConsensusCore -o /<>/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /<>/include/ConsensusCore/Feature.hpp:56: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /<>/include/ConsensusCore/Matrix/DenseMatrix.hpp:64: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /<>/include/ConsensusCore/Poa/PoaConsensus.hpp:60: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -pthread -shared -Wl,-O1 -I/<>/include -I/<>/external -I /usr/include/python2.7 -I /usr/lib/python2.7/dist-packages/numpy/core/include /<>/build/Python/ConsensusCore_wrap.cxx /<>/build/C++/libConsensusCore.a -o /<>/build/Python/_ConsensusCore.so make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' I: pybuild base:184: /usr/bin/python3 setup.py build WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig3.0 PYTHON_INCLUDE = /usr/include/python3.5m NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_ABI = c++98 make[1]: Entering directory '/<>' make -f make/Cpp.mk make[2]: Entering directory '/<>' make[2]: '/<>/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/<>' make -f make/Python.mk make[2]: Entering directory '/<>' mkdir -p /<>/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/<>/include -I/<>/external -module ConsensusCore -o /<>/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /<>/include/ConsensusCore/Feature.hpp:56: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /<>/include/ConsensusCore/Matrix/DenseMatrix.hpp:64: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /<>/include/ConsensusCore/Poa/PoaConsensus.hpp:60: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -pthread -shared -Wl,-O1 -I/<>/include -I/<>/external -I /usr/include/python3.5m -I /usr/lib/python3/dist-packages/numpy/core/include /<>/build/Python/ConsensusCore_wrap.cxx /<>/build/C++/libConsensusCore.a -o /<>/build/Python/_ConsensusCore.so make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' /usr/bin/make test make[2]: Entering directory '/<>' /usr/bin/make -f make/Cpp.mk make[3]: Entering directory '/<>' make[3]: '/<>/build/C++/libConsensusCore.a' is up to date. make[3]: Leaving directory '/<>' make[3]: Entering directory '/<>' mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestMutations.cpp -o /<>/build/Tests/TestMutations.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestPairwiseAlignment.cpp -o /<>/build/Tests/TestPairwiseAlignment.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/ParameterSettings.cpp -o /<>/build/Tests/ParameterSettings.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestRecursors.cpp -o /<>/build/Tests/TestRecursors.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestMatrixFacades.cpp -o /<>/build/Tests/TestMatrixFacades.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestDiploidQuiver.cpp -o /<>/build/Tests/TestDiploidQuiver.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestQvEvaluator.cpp -o /<>/build/Tests/TestQvEvaluator.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestMutationEnumerator.cpp -o /<>/build/Tests/TestMutationEnumerator.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestSparseVector.cpp -o /<>/build/Tests/TestSparseVector.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestMutationScorer.cpp -o /<>/build/Tests/TestMutationScorer.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestMultiReadMutationScorer.cpp -o /<>/build/Tests/TestMultiReadMutationScorer.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestCoverage.cpp -o /<>/build/Tests/TestCoverage.o mkdir -p /<>/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestPoaConsensus.cpp -o /<>/build/Tests/TestPoaConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro /<>/build/Tests/TestMutations.o /<>/build/Tests/TestPairwiseAlignment.o /<>/build/Tests/ParameterSettings.o /<>/build/Tests/TestRecursors.o /<>/build/Tests/TestMatrixFacades.o /<>/build/Tests/TestDiploidQuiver.o /<>/build/Tests/TestQvEvaluator.o /<>/build/Tests/TestMutationEnumerator.o /<>/build/Tests/TestSparseVector.o /<>/build/Tests/TestMutationScorer.o /<>/build/Tests/TestMultiReadMutationScorer.o /<>/build/Tests/TestCoverage.o /<>/build/Tests/TestPoaConsensus.o /<>/build/C++/libConsensusCore.a -I/<>/external/gmock-1.7.0 /<>/external/gmock-1.7.0/gmock-gtest-all.cc /<>/external/gmock-1.7.0/gmock_main.cc -lpthread -o /<>/build/Tests/test-runner GTEST_OUTPUT="xml:tests-summary.xml" /<>/build/Tests/test-runner Running main() from gmock_main.cc [==========] Running 158 tests from 29 test cases. [----------] Global test environment set-up. [----------] 7 tests from MutationTest [ RUN ] MutationTest.BasicTest [ OK ] MutationTest.BasicTest (0 ms) [ RUN ] MutationTest.DeleteTest [ OK ] MutationTest.DeleteTest (0 ms) [ RUN ] MutationTest.InsertTest [ OK ] MutationTest.InsertTest (0 ms) [ RUN ] MutationTest.ApplyMutationsTest [ OK ] MutationTest.ApplyMutationsTest (0 ms) [ RUN ] MutationTest.ApplyMutationsToSamePositionTest [ OK ] MutationTest.ApplyMutationsToSamePositionTest (0 ms) [ RUN ] MutationTest.MutationsToTranscript [ OK ] MutationTest.MutationsToTranscript (0 ms) [ RUN ] MutationTest.MutatedTemplatePositionsTest [ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms) [----------] 7 tests from MutationTest (4 ms total) [----------] 3 tests from PairwiseAlignmentTests [ RUN ] PairwiseAlignmentTests.RepresentationTests [ OK ] PairwiseAlignmentTests.RepresentationTests (0 ms) [ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests [ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms) [ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest [ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (0 ms) [----------] 3 tests from PairwiseAlignmentTests (2 ms total) [----------] 2 tests from AffineAlignmentTests [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest [ OK ] AffineAlignmentTests.LargeGapTest (17 ms) [----------] 2 tests from AffineAlignmentTests (18 ms total) [----------] 1 test from IupacAlignmentTests [ RUN ] IupacAlignmentTests.BasicTest [ OK ] IupacAlignmentTests.BasicTest (0 ms) [----------] 1 test from IupacAlignmentTests (0 ms total) [----------] 1 test from LinearAlignmentTests [ RUN ] LinearAlignmentTests.BasicTest [ OK ] LinearAlignmentTests.BasicTest (0 ms) [----------] 1 test from LinearAlignmentTests (0 ms total) [----------] 7 tests from RecursorTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/0.SmallMatchTest [ OK ] RecursorTest/0.SmallMatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMismatchTest [ OK ] RecursorTest/0.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMergeTest [ OK ] RecursorTest/0.SmallMergeTest (0 ms) [ RUN ] RecursorTest/0.MediumSizedTest [ OK ] RecursorTest/0.MediumSizedTest (4 ms) [ RUN ] RecursorTest/0.LinkTest [ OK ] RecursorTest/0.LinkTest (0 ms) [ RUN ] RecursorTest/0.ExtendAlphaTest [ OK ] RecursorTest/0.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/0.ExtendBetaTest [ OK ] RecursorTest/0.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/0 (8 ms total) [----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/1.SmallMatchTest [ OK ] RecursorTest/1.SmallMatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMismatchTest [ OK ] RecursorTest/1.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMergeTest [ OK ] RecursorTest/1.SmallMergeTest (0 ms) [ RUN ] RecursorTest/1.MediumSizedTest [ OK ] RecursorTest/1.MediumSizedTest (4 ms) [ RUN ] RecursorTest/1.LinkTest [ OK ] RecursorTest/1.LinkTest (0 ms) [ RUN ] RecursorTest/1.ExtendAlphaTest [ OK ] RecursorTest/1.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/1.ExtendBetaTest [ OK ] RecursorTest/1.ExtendBetaTest (1 ms) [----------] 7 tests from RecursorTest/1 (8 ms total) [----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/2.SmallMatchTest [ OK ] RecursorTest/2.SmallMatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMismatchTest [ OK ] RecursorTest/2.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMergeTest [ OK ] RecursorTest/2.SmallMergeTest (0 ms) [ RUN ] RecursorTest/2.MediumSizedTest [ OK ] RecursorTest/2.MediumSizedTest (4 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (0 ms) [ RUN ] RecursorTest/2.ExtendAlphaTest [ OK ] RecursorTest/2.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/2.ExtendBetaTest [ OK ] RecursorTest/2.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/2 (8 ms total) [----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/3.SmallMatchTest [ OK ] RecursorTest/3.SmallMatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMismatchTest [ OK ] RecursorTest/3.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest [ OK ] RecursorTest/3.MediumSizedTest (3 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/3 (8 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (114 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (116 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (127 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (41 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (41 ms) [----------] 5 tests from RecursorFuzzTest/0 (441 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (98 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (100 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (103 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (42 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (44 ms) [----------] 5 tests from RecursorFuzzTest/1 (388 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (118 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (118 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (146 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (31 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (31 ms) [----------] 5 tests from RecursorFuzzTest/2 (444 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (107 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (105 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (105 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (29 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (31 ms) [----------] 5 tests from RecursorFuzzTest/3 (377 ms total) [----------] 11 tests from MatrixTest/0, where TypeParam = ConsensusCore::DenseMatrix [ RUN ] MatrixTest/0.Basic [ OK ] MatrixTest/0.Basic (0 ms) [ RUN ] MatrixTest/0.Nullability [ OK ] MatrixTest/0.Nullability (0 ms) [ RUN ] MatrixTest/0.Ranges [ OK ] MatrixTest/0.Ranges (0 ms) [ RUN ] MatrixTest/0.IsColumnEmpty [ OK ] MatrixTest/0.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/0.SSE [ OK ] MatrixTest/0.SSE (0 ms) [ RUN ] MatrixTest/0.ToHostArray [ OK ] MatrixTest/0.ToHostArray (0 ms) [ RUN ] MatrixTest/0.NonSequentialAccess [ OK ] MatrixTest/0.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/0.Holes [ OK ] MatrixTest/0.Holes (0 ms) [ RUN ] MatrixTest/0.BigBandedMatrix N13ConsensusCore11DenseMatrixE : 1000000 [ OK ] MatrixTest/0.BigBandedMatrix (10 ms) [ RUN ] MatrixTest/0.BigIrregularBandedMatrix [ OK ] MatrixTest/0.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/0.CopyTest [ OK ] MatrixTest/0.CopyTest (0 ms) [----------] 11 tests from MatrixTest/0 (11 ms total) [----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix [ RUN ] MatrixTest/1.Basic [ OK ] MatrixTest/1.Basic (0 ms) [ RUN ] MatrixTest/1.Nullability [ OK ] MatrixTest/1.Nullability (0 ms) [ RUN ] MatrixTest/1.Ranges [ OK ] MatrixTest/1.Ranges (0 ms) [ RUN ] MatrixTest/1.IsColumnEmpty [ OK ] MatrixTest/1.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/1.SSE [ OK ] MatrixTest/1.SSE (0 ms) [ RUN ] MatrixTest/1.ToHostArray [ OK ] MatrixTest/1.ToHostArray (0 ms) [ RUN ] MatrixTest/1.NonSequentialAccess [ OK ] MatrixTest/1.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/1.Holes [ OK ] MatrixTest/1.Holes (0 ms) [ RUN ] MatrixTest/1.BigBandedMatrix N13ConsensusCore12SparseMatrixE : 1001976 [ OK ] MatrixTest/1.BigBandedMatrix (12 ms) [ RUN ] MatrixTest/1.BigIrregularBandedMatrix [ OK ] MatrixTest/1.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/1.CopyTest [ OK ] MatrixTest/1.CopyTest (0 ms) [----------] 11 tests from MatrixTest/1 (14 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (75 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (77 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (88 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (60 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (7 ms) [----------] 5 tests from QvEvaluatorTest (307 ms total) [----------] 4 tests from MutationEnumerationTest [ RUN ] MutationEnumerationTest.TestAllMutations [ OK ] MutationEnumerationTest.TestAllMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueMutations [ OK ] MutationEnumerationTest.TestUniqueMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations [ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (2 ms) [ RUN ] MutationEnumerationTest.TestDinucleotideMutations [ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) [----------] 4 tests from MutationEnumerationTest (3 ms total) [----------] 2 tests from SparseVectorTest [ RUN ] SparseVectorTest.BasicTest [ OK ] SparseVectorTest.BasicTest (0 ms) [ RUN ] SparseVectorTest.BasicTest2 [ OK ] SparseVectorTest.BasicTest2 (0 ms) [----------] 2 tests from SparseVectorTest (0 ms total) [----------] 1 test from SparseVector [ RUN ] SparseVector.CopyTest [ OK ] SparseVector.CopyTest (0 ms) [----------] 1 test from SparseVector (0 ms total) [----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/0.BasicTest [ OK ] MutationScorerTest/0.BasicTest (1 ms) [ RUN ] MutationScorerTest/0.CopyTest [ OK ] MutationScorerTest/0.CopyTest (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtBeginning [ OK ] MutationScorerTest/0.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtEnd [ OK ] MutationScorerTest/0.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/0.TinyTemplate [ OK ] MutationScorerTest/0.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/0.TemplateMutationWorkflow [ OK ] MutationScorerTest/0.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideInsertionTest [ OK ] MutationScorerTest/0.DinucleotideInsertionTest (3 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/0 (6 ms total) [----------] 8 tests from MutationScorerTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/1.BasicTest [ OK ] MutationScorerTest/1.BasicTest (0 ms) [ RUN ] MutationScorerTest/1.CopyTest [ OK ] MutationScorerTest/1.CopyTest (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtBeginning [ OK ] MutationScorerTest/1.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtEnd [ OK ] MutationScorerTest/1.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/1.TinyTemplate [ OK ] MutationScorerTest/1.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/1.TemplateMutationWorkflow [ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideInsertionTest [ OK ] MutationScorerTest/1.DinucleotideInsertionTest (3 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/1 (6 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest [ OK ] MutationScorerTest/2.BasicTest (1 ms) [ RUN ] MutationScorerTest/2.CopyTest [ OK ] MutationScorerTest/2.CopyTest (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtBeginning [ OK ] MutationScorerTest/2.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtEnd [ OK ] MutationScorerTest/2.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/2.TinyTemplate [ OK ] MutationScorerTest/2.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/2.TemplateMutationWorkflow [ OK ] MutationScorerTest/2.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (3 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/2 (6 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest [ OK ] MutationScorerTest/3.BasicTest (1 ms) [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning [ OK ] MutationScorerTest/3.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (1 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest [ OK ] MutationScorerTest/3.DinucleotideInsertionTest (3 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest [ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/3 (6 ms total) [----------] 1 test from QuiverConfigTableTests [ RUN ] QuiverConfigTableTests.IllegalChemistry [ OK ] QuiverConfigTableTests.IllegalChemistry (0 ms) [----------] 1 test from QuiverConfigTableTests (0 ms total) [----------] 3 tests from MutationOrientationTests [ RUN ] MutationOrientationTests.ReadScoresMutation1 [ OK ] MutationOrientationTests.ReadScoresMutation1 (0 ms) [ RUN ] MutationOrientationTests.ReadScoresMutation2 [ OK ] MutationOrientationTests.ReadScoresMutation2 (0 ms) [ RUN ] MutationOrientationTests.OrientedMutation [ OK ] MutationOrientationTests.OrientedMutation (0 ms) [----------] 3 tests from MutationOrientationTests (0 ms total) [----------] 11 tests from MultiReadMutationScorerTest/0, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MultiReadMutationScorerTest/0.Template [ OK ] MultiReadMutationScorerTest/0.Template (0 ms) [ RUN ] MultiReadMutationScorerTest/0.BasicTest [ OK ] MultiReadMutationScorerTest/0.BasicTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest [ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (2 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest [ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (2 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 [ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (2 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest [ OK ] MultiReadMutationScorerTest/0.CopyTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (1 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms) [----------] 11 tests from MultiReadMutationScorerTest/0 (8 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (1 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest2 [ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) [----------] 3 tests from CoverageTests (1 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest [ OK ] PoaGraph.SmallBasicTest (1 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (0 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (1 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (0 ms) [----------] 4 tests from PoaGraph (2 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (0 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (0 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (1 ms) [ RUN ] PoaConsensus.SmallTilingTest [ OK ] PoaConsensus.SmallTilingTest (0 ms) [ RUN ] PoaConsensus.TestVerboseGraphVizOutput [ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png sh: 1: dot: not found [ OK ] PoaConsensus.TestLocalStaggered (6 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (0 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (955 ms) [----------] 8 tests from PoaConsensus (963 ms total) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (3050 ms total) [ PASSED ] 158 tests. make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python2,python3 --buildsystem=pybuild create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:184: /usr/bin/python setup.py install --root /<>/debian/python-pbconsensuscore WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig3.0 PYTHON_INCLUDE = /usr/include/python2.7 NUMPY_INCLUDE = /usr/lib/python2.7/dist-packages/numpy/core/include DEBUG = CPP_ABI = c++98 make[1]: Entering directory '/<>' make -f make/Cpp.mk make[2]: Entering directory '/<>' make[2]: '/<>/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/<>' make -f make/Python.mk make[2]: Entering directory '/<>' mkdir -p /<>/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/<>/include -I/<>/external -module ConsensusCore -o /<>/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /<>/include/ConsensusCore/Feature.hpp:56: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /<>/include/ConsensusCore/Matrix/DenseMatrix.hpp:64: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /<>/include/ConsensusCore/Poa/PoaConsensus.hpp:60: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -pthread -shared -Wl,-O1 -I/<>/include -I/<>/external -I /usr/include/python2.7 -I /usr/lib/python2.7/dist-packages/numpy/core/include /<>/build/Python/ConsensusCore_wrap.cxx /<>/build/C++/libConsensusCore.a -o /<>/build/Python/_ConsensusCore.so make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' running install running install_lib running build_py copying build/Python/ConsensusCore.py -> /<>/.pybuild/pythonX.Y_2.7/build copying build/Python/_ConsensusCore.so -> /<>/.pybuild/pythonX.Y_2.7/build creating /<>/debian/python-pbconsensuscore/usr creating /<>/debian/python-pbconsensuscore/usr/lib creating /<>/debian/python-pbconsensuscore/usr/lib/python2.7 creating /<>/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages copying /<>/.pybuild/pythonX.Y_2.7/build/ConsensusCore.py -> /<>/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages copying /<>/.pybuild/pythonX.Y_2.7/build/_ConsensusCore.so -> /<>/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages byte-compiling /<>/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages/ConsensusCore.py to ConsensusCore.pyc running install_egg_info running egg_info creating build/Python/ConsensusCore.egg-info writing build/Python/ConsensusCore.egg-info/PKG-INFO writing top-level names to build/Python/ConsensusCore.egg-info/top_level.txt writing dependency_links to build/Python/ConsensusCore.egg-info/dependency_links.txt writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' reading manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' Copying build/Python/ConsensusCore.egg-info to /<>/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:184: /usr/bin/python3 setup.py install --root /<>/debian/python3-pbconsensuscore WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig3.0 PYTHON_INCLUDE = /usr/include/python3.5m NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_ABI = c++98 make[1]: Entering directory '/<>' make -f make/Cpp.mk make[2]: Entering directory '/<>' make[2]: '/<>/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/<>' make -f make/Python.mk make[2]: Entering directory '/<>' mkdir -p /<>/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/<>/include -I/<>/external -module ConsensusCore -o /<>/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /<>/include/ConsensusCore/Feature.hpp:56: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /<>/include/ConsensusCore/Matrix/DenseMatrix.hpp:64: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /<>/include/ConsensusCore/Poa/PoaConsensus.hpp:60: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/include -I/<>/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -pthread -shared -Wl,-O1 -I/<>/include -I/<>/external -I /usr/include/python3.5m -I /usr/lib/python3/dist-packages/numpy/core/include /<>/build/Python/ConsensusCore_wrap.cxx /<>/build/C++/libConsensusCore.a -o /<>/build/Python/_ConsensusCore.so make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' running install running install_lib running build_py copying build/Python/ConsensusCore.py -> /<>/.pybuild/pythonX.Y_3.5/build copying build/Python/_ConsensusCore.so -> /<>/.pybuild/pythonX.Y_3.5/build creating /<>/debian/python3-pbconsensuscore/usr creating /<>/debian/python3-pbconsensuscore/usr/lib creating /<>/debian/python3-pbconsensuscore/usr/lib/python3.5 creating /<>/debian/python3-pbconsensuscore/usr/lib/python3.5/dist-packages copying /<>/.pybuild/pythonX.Y_3.5/build/ConsensusCore.py -> /<>/debian/python3-pbconsensuscore/usr/lib/python3.5/dist-packages copying /<>/.pybuild/pythonX.Y_3.5/build/_ConsensusCore.so -> /<>/debian/python3-pbconsensuscore/usr/lib/python3.5/dist-packages byte-compiling /<>/debian/python3-pbconsensuscore/usr/lib/python3.5/dist-packages/ConsensusCore.py to ConsensusCore.cpython-35.pyc running install_egg_info running egg_info writing top-level names to build/Python/ConsensusCore.egg-info/top_level.txt writing dependency_links to build/Python/ConsensusCore.egg-info/dependency_links.txt writing build/Python/ConsensusCore.egg-info/PKG-INFO reading manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' Copying build/Python/ConsensusCore.egg-info to /<>/debian/python3-pbconsensuscore/usr/lib/python3.5/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts dh_install -a -O--buildsystem=pybuild dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_python2 make[1]: Entering directory '/<>' dh_python2 I: dh_python2 fs:322: renaming _ConsensusCore.so to _ConsensusCore.i386-linux-gnu.so dh_numpy make[1]: Leaving directory '/<>' debian/rules override_dh_python3 make[1]: Entering directory '/<>' dh_python3 I: dh_python3 fs:85: renaming debian/python3-pbconsensuscore/usr/lib/python3.5/dist-packages/_ConsensusCore.so to debian/python3-pbconsensuscore/usr/lib/python3.5/dist-packages/_ConsensusCore.cpython-35m-i386-linux-gnu.so dh_numpy3 make[1]: Leaving directory '/<>' dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild Normalizing debian/libconsensuscore-dev/usr/lib/i386-linux-gnu/libConsensusCore.a dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages/_ConsensusCore.i386-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-pbconsensuscore/usr/lib/python3/dist-packages/_ConsensusCore.cpython-35m-i386-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package libconsensuscore-dev: unknown substitution variable ${shlibs:Depends} dpkg-gencontrol: warning: package libconsensuscore-dev: unused substitution variable ${python:Depends} dpkg-gencontrol: warning: package libconsensuscore-dev: unused substitution variable ${python3:Depends} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python:Versions} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python3:Depends} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python3:Versions} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python:Depends} dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgstriptranslations for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgmaintainermangler for PPA build INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.0.2-2build1_i386.deb'. INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.0.2-2build1_i386.deb'. INFO: Disabling pkgstripfiles for PPA build dpkg-deb: building package 'python-pbconsensuscore' in '../python-pbconsensuscore_1.0.2-2build1_i386.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../consensuscore_1.0.2-2build1_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build consensuscore-1.0.2 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170512-1109 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ consensuscore_1.0.2-2build1_i386.changes: ----------------------------------------- Format: 1.8 Date: Fri, 12 May 2017 16:25:16 +0530 Source: consensuscore Binary: libconsensuscore-dev python-pbconsensuscore python3-pbconsensuscore Architecture: i386 Version: 1.0.2-2build1 Distribution: artful Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Bhavani Shankar Description: libconsensuscore-dev - algorithms for PacBio multiple sequence consensus -- development python-pbconsensuscore - algorithms for PacBio multiple sequence consensus -- Python 2 python3-pbconsensuscore - algorithms for PacBio multiple sequence consensus -- Python 3 Changes: consensuscore (1.0.2-2build1) artful; urgency=medium . * Rebuild to add support for python 3.6. Checksums-Sha1: 368b1f1f03cc6e36baa8e97747643dfa0b64c266 7020 consensuscore_1.0.2-2build1_i386.buildinfo fec0d59814d6bff9d099feaea038d13876a8a826 462900 libconsensuscore-dev_1.0.2-2build1_i386.deb a667c120d72dc4cf5c65937d3b9387c007a501f2 643584 python-pbconsensuscore_1.0.2-2build1_i386.deb c76e2888fddae7c6fd64bed419bfc4472877fd0f 645498 python3-pbconsensuscore_1.0.2-2build1_i386.deb Checksums-Sha256: d749e31430c67205f70f3ef73ccd325ba307fdf96322d68e6e3c2a5e83280dcc 7020 consensuscore_1.0.2-2build1_i386.buildinfo d9af93c48cde723c3af556deaebd738fd3eac10116bd2eab55c52fcc392be065 462900 libconsensuscore-dev_1.0.2-2build1_i386.deb e506a691254c18e26d5487a23cd14f23639b875e2b8fdf06c4cc3bf7ea971916 643584 python-pbconsensuscore_1.0.2-2build1_i386.deb 9bee3d7e906a52390581d08f2b81ab933cec348144b1b9389a0b5f2e726b8d1f 645498 python3-pbconsensuscore_1.0.2-2build1_i386.deb Files: da0e66ce23c8efd46ea1f7579ff8df2b 7020 science optional consensuscore_1.0.2-2build1_i386.buildinfo 96ca8be1856fa10bec3bad8a371b2cea 462900 libdevel optional libconsensuscore-dev_1.0.2-2build1_i386.deb ee55cdae018a82058f2170a0031312c2 643584 python optional python-pbconsensuscore_1.0.2-2build1_i386.deb 8c4d57d39b2d7135aa385f568ad760f2 645498 python optional python3-pbconsensuscore_1.0.2-2build1_i386.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libconsensuscore-dev_1.0.2-2build1_i386.deb ------------------------------------------- new debian package, version 2.0. size 462900 bytes: control archive=2171 bytes. 734 bytes, 17 lines control 4237 bytes, 52 lines md5sums Package: libconsensuscore-dev Source: consensuscore Version: 1.0.2-2build1 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 3072 Section: libdevel Priority: optional Homepage: https://github.com/PacificBiosciences/ConsensusCore Description: algorithms for PacBio multiple sequence consensus -- development files ConsensusCore is a library of C++ algorithms for Pacific Biosciences multiple sequence consensus that powers Quiver (Python) and ConsensusTools (.NET). This library primarily exists as the backend for GenomicConsensus, which implements Quiver. . This package is part of the SMRT Analysis suite. It provides the header files and static library. drwxr-xr-x root/root 0 2017-05-12 10:55 ./ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/ drwxr-xr-x root/root 0 2016-05-06 17:25 ./usr/include/ drwxr-xr-x root/root 0 2016-05-06 17:25 ./usr/include/ConsensusCore/ drwxr-xr-x root/root 0 2016-05-06 17:25 ./usr/include/ConsensusCore/Align/ -rw-r--r-- root/root 3305 2016-05-06 17:25 ./usr/include/ConsensusCore/Align/AffineAlignment.hpp -rw-r--r-- root/root 2713 2016-05-06 17:25 ./usr/include/ConsensusCore/Align/AlignConfig.hpp -rw-r--r-- root/root 2468 2016-05-06 17:25 ./usr/include/ConsensusCore/Align/LinearAlignment.hpp -rw-r--r-- root/root 4044 2016-05-06 17:25 ./usr/include/ConsensusCore/Align/PairwiseAlignment.hpp -rw-r--r-- root/root 1989 2016-05-06 17:25 ./usr/include/ConsensusCore/Checksum.hpp -rw-r--r-- root/root 2813 2016-05-06 17:25 ./usr/include/ConsensusCore/Coverage.hpp drwxr-xr-x root/root 0 2016-05-06 17:25 ./usr/include/ConsensusCore/Edna/ -rw-r--r-- root/root 2716 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./usr/share/doc/libconsensuscore-dev/copyright python-pbconsensuscore_1.0.2-2build1_i386.deb --------------------------------------------- new debian package, version 2.0. size 643584 bytes: control archive=1183 bytes. 907 bytes, 18 lines control 683 bytes, 7 lines md5sums 172 bytes, 9 lines * postinst #!/bin/sh 281 bytes, 14 lines * prerm #!/bin/sh Package: python-pbconsensuscore Source: consensuscore Version: 1.0.2-2build1 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 2743 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.0), libstdc++6 (>= 5.2), python (<< 2.8), python (>= 2.7~), python-numpy (>= 1:1.10.0~b1), python-numpy-abi9, python:any (<< 2.8), python:any (>= 2.7.5-5~) Section: python Priority: optional Homepage: https://github.com/PacificBiosciences/ConsensusCore Description: algorithms for PacBio multiple sequence consensus -- Python 2 ConsensusCore is a library of C++ algorithms for Pacific Biosciences multiple sequence consensus that powers Quiver (Python) and ConsensusTools (.NET). This library primarily exists as the backend for GenomicConsensus, which implements Quiver. . This package is part of the SMRT Analysis suite. It provides the Python2 bindings. drwxr-xr-x root/root 0 2017-05-12 10:55 ./ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/lib/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/lib/python2.7/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/lib/python2.7/dist-packages/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/lib/python2.7/dist-packages/ConsensusCore-1.0.2.egg-info/ -rw-r--r-- root/root 1985 2017-05-12 10:55 ./usr/lib/python2.7/dist-packages/ConsensusCore-1.0.2.egg-info/PKG-INFO -rw-r--r-- root/root 1 2017-05-12 10:55 ./usr/lib/python2.7/dist-packages/ConsensusCore-1.0.2.egg-info/dependency_links.txt -rw-r--r-- root/root 15 2017-05-12 10:55 ./usr/lib/python2.7/dist-packages/ConsensusCore-1.0.2.egg-info/top_level.txt -rw-r--r-- root/root 3439 2017-05-12 10:55 ./usr/lib/python2.7/dist-packages/ConsensusCore.py -rw-r--r-- root/root 2780816 2017-05-12 10:55 ./usr/lib/python2.7/dist-packages/_ConsensusCore.i386-linux-gnu.so drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/share/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/share/doc/python-pbconsensuscore/ -rw-r--r-- root/root 648 2017-05-12 10:55 ./usr/share/doc/python-pbconsensuscore/changelog.Debian.gz -rw-r--r-- root/root 5835 2016-07-13 14:15 ./usr/share/doc/python-pbconsensuscore/copyright python3-pbconsensuscore_1.0.2-2build1_i386.deb ---------------------------------------------- new debian package, version 2.0. size 645498 bytes: control archive=1262 bytes. 892 bytes, 18 lines control 687 bytes, 7 lines md5sums 175 bytes, 9 lines * postinst #!/bin/sh 421 bytes, 12 lines * prerm #!/bin/sh Package: python3-pbconsensuscore Source: consensuscore Version: 1.0.2-2build1 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 2751 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.0), libstdc++6 (>= 5.2), python3 (<< 3.6), python3 (>= 3.5~), python3-numpy (>= 1:1.10.0~b1), python3-numpy-abi9, python3:any (>= 3.3.2-2~) Section: python Priority: optional Homepage: https://github.com/PacificBiosciences/ConsensusCore Description: algorithms for PacBio multiple sequence consensus -- Python 3 ConsensusCore is a library of C++ algorithms for Pacific Biosciences multiple sequence consensus that powers Quiver (Python) and ConsensusTools (.NET). This library primarily exists as the backend for GenomicConsensus, which implements Quiver. . This package is part of the SMRT Analysis suite. It provides the Python3 bindings. drwxr-xr-x root/root 0 2017-05-12 10:55 ./ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/lib/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/lib/python3/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/lib/python3/dist-packages/ConsensusCore-1.0.2.egg-info/ -rw-r--r-- root/root 1985 2017-05-12 10:55 ./usr/lib/python3/dist-packages/ConsensusCore-1.0.2.egg-info/PKG-INFO -rw-r--r-- root/root 1 2017-05-12 10:55 ./usr/lib/python3/dist-packages/ConsensusCore-1.0.2.egg-info/dependency_links.txt -rw-r--r-- root/root 15 2017-05-12 10:55 ./usr/lib/python3/dist-packages/ConsensusCore-1.0.2.egg-info/top_level.txt -rw-r--r-- root/root 3439 2017-05-12 10:55 ./usr/lib/python3/dist-packages/ConsensusCore.py -rw-r--r-- root/root 2788848 2017-05-12 10:55 ./usr/lib/python3/dist-packages/_ConsensusCore.cpython-35m-i386-linux-gnu.so drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/share/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-05-12 10:55 ./usr/share/doc/python3-pbconsensuscore/ -rw-r--r-- root/root 648 2017-05-12 10:55 ./usr/share/doc/python3-pbconsensuscore/changelog.Debian.gz -rw-r--r-- root/root 5835 2016-07-13 14:15 ./usr/share/doc/python3-pbconsensuscore/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 160364 Build-Time: 584 Distribution: artful Host Architecture: i386 Install-Time: 43 Job: consensuscore_1.0.2-2build1.dsc Machine Architecture: amd64 Package: consensuscore Package-Time: 627 Source-Version: 1.0.2-2build1 Space: 160364 Status: successful Version: 1.0.2-2build1 -------------------------------------------------------------------------------- Finished at 20170512-1109 Build needed 00:10:27, 160364k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12573691'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12573691/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12573691'] Unmounting chroot for build PACKAGEBUILD-12573691... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12573691'] Removing build PACKAGEBUILD-12573691