RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-05 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 11:12:29 ntpdate[1797]: adjust time server 10.211.37.1 offset -0.002748 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-12573736', '/home/buildd/filecache-default/e3a0751dad18cad81698aa46cb02fd9a2acf7c0b'] Unpacking chroot for build PACKAGEBUILD-12573736 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-12573736'] Mounting chroot for build PACKAGEBUILD-12573736 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-12573736', 'deb http://ftpmaster.internal/ubuntu artful main universe', 'deb http://ftpmaster.internal/ubuntu artful-security main universe', 'deb http://ftpmaster.internal/ubuntu artful-updates main universe', 'deb http://ftpmaster.internal/ubuntu artful-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-12573736 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-12573736', 'amd64'] Updating debian chroot for build PACKAGEBUILD-12573736 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://ftpmaster.internal/ubuntu artful-proposed InRelease [235 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main amd64 Packages [1168 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main Translation-en [564 kB] Get:7 http://ftpmaster.internal/ubuntu artful/universe amd64 Packages [8278 kB] Get:8 http://ftpmaster.internal/ubuntu artful/universe Translation-en [4747 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 Packages [84.5 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main Translation-en [41.4 kB] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/universe amd64 Packages [149 kB] Get:12 http://ftpmaster.internal/ubuntu artful-proposed/universe Translation-en [82.3 kB] Fetched 15.7 MB in 5s (2706 kB/s) Reading package lists... 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: advancecomp apt apt-transport-https binutils cpp-6 debianutils dmsetup dpkg dpkg-dev g++-6 gcc-6 gcc-6-base init init-system-helpers libapparmor1 libapt-pkg5.0 libasan3 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 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 liblsan0 libmpx2 libquadmath0 libroken18-heimdal libselinux1 libstdc++-6-dev libstdc++6 libsystemd0 libtsan0 libubsan0 libudev1 libusb-0.1-4 libwind0-heimdal linux-libc-dev systemd systemd-sysv 53 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 38.7 MB of archives. After this operation, 697 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu artful/main amd64 debianutils amd64 4.8.1.1 [85.6 kB] Get:2 http://ftpmaster.internal/ubuntu artful/main amd64 dpkg amd64 1.18.23ubuntu6 [1132 kB] Get:3 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 init-system-helpers all 1.48 [37.8 kB] Get:4 http://ftpmaster.internal/ubuntu artful/main amd64 gcc-7-base amd64 7.1.0-4ubuntu1 [18.4 kB] Get:5 http://ftpmaster.internal/ubuntu artful/main amd64 libgcc1 amd64 1:7.1.0-4ubuntu1 [39.3 kB] Get:6 http://ftpmaster.internal/ubuntu artful/main amd64 libstdc++6 amd64 7.1.0-4ubuntu1 [403 kB] Get:7 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libapt-pkg5.0 amd64 1.4.3 [785 kB] Get:8 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 apt amd64 1.4.3 [1096 kB] Get:9 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libapparmor1 amd64 2.11.0-2ubuntu6 [30.1 kB] Get:10 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libaudit-common all 1:2.6.6-1ubuntu2 [4626 B] Get:11 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libaudit1 amd64 1:2.6.6-1ubuntu2 [37.6 kB] Get:12 http://ftpmaster.internal/ubuntu artful/main amd64 libkmod2 amd64 24-1ubuntu1 [39.9 kB] Get:13 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 libselinux1 amd64 2.6-3build1 [67.5 kB] Get:14 http://ftpmaster.internal/ubuntu artful/main amd64 systemd amd64 233-6ubuntu1 [2443 kB] Get:15 http://ftpmaster.internal/ubuntu artful/main amd64 libsystemd0 amd64 233-6ubuntu1 [213 kB] Get:16 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 init amd64 1.48 [5806 B] Get:17 http://ftpmaster.internal/ubuntu artful/main amd64 systemd-sysv amd64 233-6ubuntu1 [13.6 kB] Get:18 http://ftpmaster.internal/ubuntu artful/main amd64 libudev1 amd64 233-6ubuntu1 [58.1 kB] Get:19 http://ftpmaster.internal/ubuntu artful/main amd64 libdevmapper1.02.1 amd64 2:1.02.137-2ubuntu1 [135 kB] Get:20 http://ftpmaster.internal/ubuntu artful/main amd64 dmsetup amd64 2:1.02.137-2ubuntu1 [71.8 kB] Get:21 http://ftpmaster.internal/ubuntu artful/main amd64 libroken18-heimdal amd64 7.1.0+dfsg-13 [40.8 kB] Get:22 http://ftpmaster.internal/ubuntu artful/main amd64 libasn1-8-heimdal amd64 7.1.0+dfsg-13 [176 kB] Get:23 http://ftpmaster.internal/ubuntu artful/main amd64 libgnutls30 amd64 3.5.8-5ubuntu1 [675 kB] Get:24 http://ftpmaster.internal/ubuntu artful/main amd64 libheimbase1-heimdal amd64 7.1.0+dfsg-13 [29.1 kB] Get:25 http://ftpmaster.internal/ubuntu artful/main amd64 libhcrypto4-heimdal amd64 7.1.0+dfsg-13 [88.1 kB] Get:26 http://ftpmaster.internal/ubuntu artful/main amd64 libwind0-heimdal amd64 7.1.0+dfsg-13 [47.9 kB] Get:27 http://ftpmaster.internal/ubuntu artful/main amd64 libhx509-5-heimdal amd64 7.1.0+dfsg-13 [107 kB] Get:28 http://ftpmaster.internal/ubuntu artful/main amd64 libkrb5-26-heimdal amd64 7.1.0+dfsg-13 [206 kB] Get:29 http://ftpmaster.internal/ubuntu artful/main amd64 libheimntlm0-heimdal amd64 7.1.0+dfsg-13 [15.1 kB] Get:30 http://ftpmaster.internal/ubuntu artful/main amd64 libgssapi3-heimdal amd64 7.1.0+dfsg-13 [97.5 kB] Get:31 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 apt-transport-https amd64 1.4.3 [34.2 kB] Get:32 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 advancecomp amd64 1.23-1 [197 kB] Get:33 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 binutils amd64 2.28-5ubuntu1 [2434 kB] Get:34 http://ftpmaster.internal/ubuntu artful/main amd64 libquadmath0 amd64 7.1.0-4ubuntu1 [133 kB] Get:35 http://ftpmaster.internal/ubuntu artful/main amd64 libitm1 amd64 7.1.0-4ubuntu1 [27.5 kB] Get:36 http://ftpmaster.internal/ubuntu artful/main amd64 libmpx2 amd64 7.1.0-4ubuntu1 [11.7 kB] Get:37 http://ftpmaster.internal/ubuntu artful/main amd64 liblsan0 amd64 7.1.0-4ubuntu1 [126 kB] Get:38 http://ftpmaster.internal/ubuntu artful/main amd64 libtsan0 amd64 7.1.0-4ubuntu1 [275 kB] Get:39 http://ftpmaster.internal/ubuntu artful/main amd64 libubsan0 amd64 7.1.0-4ubuntu1 [119 kB] Get:40 http://ftpmaster.internal/ubuntu artful/main amd64 libcilkrts5 amd64 7.1.0-4ubuntu1 [42.3 kB] Get:41 http://ftpmaster.internal/ubuntu artful/main amd64 libgomp1 amd64 7.1.0-4ubuntu1 [76.1 kB] Get:42 http://ftpmaster.internal/ubuntu artful/main amd64 libatomic1 amd64 7.1.0-4ubuntu1 [8904 B] Get:43 http://ftpmaster.internal/ubuntu artful/main amd64 libasan3 amd64 6.3.0-17ubuntu1 [316 kB] Get:44 http://ftpmaster.internal/ubuntu artful/main amd64 g++-6 amd64 6.3.0-17ubuntu1 [7394 kB] Get:45 http://ftpmaster.internal/ubuntu artful/main amd64 libstdc++-6-dev amd64 6.3.0-17ubuntu1 [1407 kB] Get:46 http://ftpmaster.internal/ubuntu artful/main amd64 gcc-6 amd64 6.3.0-17ubuntu1 [7215 kB] Get:47 http://ftpmaster.internal/ubuntu artful/main amd64 libgcc-6-dev amd64 6.3.0-17ubuntu1 [2310 kB] Get:48 http://ftpmaster.internal/ubuntu artful/main amd64 libcc1-0 amd64 7.1.0-4ubuntu1 [38.5 kB] Get:49 http://ftpmaster.internal/ubuntu artful/main amd64 cpp-6 amd64 6.3.0-17ubuntu1 [6610 kB] Get:50 http://ftpmaster.internal/ubuntu artful/main amd64 gcc-6-base amd64 6.3.0-17ubuntu1 [17.1 kB] Get:51 http://ftpmaster.internal/ubuntu artful/main amd64 dpkg-dev all 1.18.23ubuntu6 [607 kB] Get:52 http://ftpmaster.internal/ubuntu artful/main amd64 libdpkg-perl all 1.18.23ubuntu6 [209 kB] Get:53 http://ftpmaster.internal/ubuntu artful/main amd64 libusb-0.1-4 amd64 2:0.1.12-31 [17.1 kB] Get:54 http://ftpmaster.internal/ubuntu artful-proposed/main amd64 linux-libc-dev amd64 4.10.0-21.23 [914 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 38.7 MB in 1s (19.7 MB/s) (Reading database ... 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Installing new version of config file /etc/systemd/resolved.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.hostname1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.locale1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.login1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.network1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.resolve1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.systemd1.conf ... Removing obsolete conffile /etc/dbus-1/system.d/org.freedesktop.timedate1.conf ... (Reading database ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-12573736', 'amd64', 'artful-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=artful-proposed', '--purge=never', '--nolog', '-A', 'consensuscore_1.0.2-2build1.dsc'] Initiating build PACKAGEBUILD-12573736 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 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-05.buildd +==============================================================================+ | consensuscore 1.0.2-2build1 (amd64) 12 May 2017 11:13 | +==============================================================================+ Package: consensuscore Version: 1.0.2-2build1 Source Version: 1.0.2-2build1 Distribution: artful-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/consensuscore-jiSl0S/consensuscore-1.0.2' with '<>' I: NOTICE: Log filtering will replace 'build/consensuscore-jiSl0S' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-12573736/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-Q4FANY/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-Q4FANY/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Q4FANY/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Q4FANY/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Q4FANY/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-Q4FANY/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (207 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 778 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-Q4FANY/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 778 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (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 ... 12498 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... 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-oX4iDE/apt_archive/sbuild-build-depends-consensuscore-dummy.deb'. Ign:1 copy:/<>/resolver-oX4iDE/apt_archive ./ InRelease Get:2 copy:/<>/resolver-oX4iDE/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-oX4iDE/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-oX4iDE/apt_archive ./ Sources [270 B] Get:5 copy:/<>/resolver-oX4iDE/apt_archive ./ Packages [591 B] Fetched 2980 B in 0s (193 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 libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-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 python3.6 python3.6-dev python3.6-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 python3.6-venv python3.6-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 libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-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 python3.6 python3.6-dev python3.6-minimal sbuild-build-depends-consensuscore-dummy swig swig3.0 0 upgraded, 87 newly installed, 1 to remove and 0 not upgraded. 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No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-2ubuntu1) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up m4 (1.4.18-1) ... Setting up libicu57:amd64 (57.1-6) ... Setting up libbsd0:amd64 (0.8.3-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-2.2build1) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:amd64 (1:5.30-1) ... Setting up libcroco3:amd64 (0.6.11-3) ... Setting up libpython3.6-minimal:amd64 (3.6.1-1) ... 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:amd64 (2.2.0-2) ... Setting up libboost-dev:amd64 (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:amd64 (2.7.13-2) ... Setting up autopoint (0.19.8.1-2ubuntu1) ... Setting up libmpdec2:amd64 (2.4.2-1) ... Setting up libfile-stripnondeterminism-perl (0.033-2) ... Setting up libpython3.6-stdlib:amd64 (3.6.1-1) ... 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:amd64 (3.5.3-1) ... Setting up python3.6-minimal (3.6.1-1) ... Setting up python2.7 (2.7.13-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libpython2.7:amd64 (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:amd64 (2.7.13-2) ... Setting up python2.7-dev (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up libpython3.6:amd64 (3.6.1-1) ... Setting up libtool (2.4.6-2) ... Setting up python3.5 (3.5.3-1) ... Setting up libpython3-stdlib:amd64 (3.5.3-1ubuntu3) ... Setting up libpython-dev:amd64 (2.7.13-2) ... Setting up python3.6 (3.6.1-1) ... Setting up po-debconf (1.0.20) ... Setting up libpython3.5:amd64 (3.5.3-1) ... Setting up python-dev (2.7.13-2) ... Setting up libpython-all-dev:amd64 (2.7.13-2) ... Setting up python-pkg-resources (33.1.1-1) ... Setting up libpython3.6-dev:amd64 (3.6.1-1) ... Setting up libpython3.5-dev:amd64 (3.5.3-1) ... Setting up python-numpy (1:1.12.1-1ubuntu2) ... Setting up python3.6-dev (3.6.1-1) ... Setting up python3.5-dev (3.5.3-1) ... Setting up python-all (2.7.13-2) ... Setting up libpython3-dev:amd64 (3.5.3-1ubuntu3) ... Setting up python-setuptools (33.1.1-1) ... Setting up python-all-dev (2.7.13-2) ... Setting up libpython3-all-dev:amd64 (3.5.3-1ubuntu3) ... Setting up dh-autoreconf (14) ... Setting up python3 (3.5.3-1ubuntu3) ... Setting up python3-numpy (1:1.12.1-1ubuntu2) ... Setting up python3-dev (3.5.3-1ubuntu3) ... Setting up python3-pkg-resources (33.1.1-1) ... Setting up dh-strip-nondeterminism (0.033-2) ... Setting up python3-all (3.5.3-1ubuntu3) ... 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 (3.5.3-1ubuntu3) ... 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 ... 32475 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 (x86_64) Toolchain package versions: binutils_2.28-5ubuntu1 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_4.10.0-21.23 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.23-1 apt_1.4.3 apt-transport-https_1.4.3 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_2.28-5ubuntu1 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_1:5.30-1 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_1.48 init-system-helpers_1.48 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.11.0-2ubuntu6 libapt-pkg5.0_1.4.3 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_1:2.6.6-1ubuntu2 libaudit1_1:2.6.6-1ubuntu2 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-4build1 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 libgnutls30_3.5.8-5ubuntu1 libgomp1_7.1.0-4ubuntu1 libgpg-error0_1.26-2 libgssapi-krb5-2_1.15-2 libgssapi3-heimdal_7.1.0+dfsg-13 libhcrypto4-heimdal_7.1.0+dfsg-13 libheimbase1-heimdal_7.1.0+dfsg-13 libheimntlm0-heimdal_7.1.0+dfsg-13 libhogweed4_3.3-1 libhx509-5-heimdal_7.1.0+dfsg-13 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0-3ubuntu2 libisl15_0.18-1 libitm1_7.1.0-4ubuntu1 libk5crypto3_1.15-2 libkeyutils1_1.5.9-9ubuntu1 libkmod2_24-1ubuntu1 libkrb5-26-heimdal_7.1.0+dfsg-13 libkrb5-3_1.15-2 libkrb5support0_1.15-2 libksba8_1.3.5-2 liblapack3_3.7.0-1 libldap-2.4-2_2.4.44+dfsg-4ubuntu1 libldap-common_2.4.44+dfsg-4ubuntu1 liblockfile-bin_1.14-1 liblockfile1_1.14-1 liblsan0_7.1.0-4ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29-1ubuntu2 libmpc3_1.0.3-1 libmpdec2_2.4.2-1 libmpfr4_3.1.5-1 libmpx2_7.1.0-4ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.3-1 libp11-kit0_0.23.3-5 libpam-modules_1.1.8-3.2ubuntu3 libpam-modules-bin_1.1.8-3.2ubuntu3 libpam-runtime_1.1.8-3.2ubuntu3 libpam0g_1.1.8-3.2ubuntu3 libpcre3_2:8.39-3 libperl5.24_5.24.1-2ubuntu1 libpipeline1_1.4.1-2 libpng16-16_1.6.29-2 libprocps6_2:3.3.12-1ubuntu2 libpsl5_0.17.0-4 libpython-all-dev_2.7.13-2 libpython-dev_2.7.13-2 libpython-stdlib_2.7.13-2 libpython2.7_2.7.13-2 libpython2.7-dev_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libpython3-all-dev_3.5.3-1ubuntu3 libpython3-dev_3.5.3-1ubuntu3 libpython3-stdlib_3.5.3-1ubuntu3 libpython3.5_3.5.3-1 libpython3.5-dev_3.5.3-1 libpython3.5-minimal_3.5.3-1 libpython3.5-stdlib_3.5.3-1 libpython3.6_3.6.1-1 libpython3.6-dev_3.6.1-1 libpython3.6-minimal_3.6.1-1 libpython3.6-stdlib_3.6.1-1 libquadmath0_7.1.0-4ubuntu1 libreadline7_7.0-0ubuntu2 libroken18-heimdal_7.1.0+dfsg-13 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-2ubuntu1 libseccomp2_2.3.1-2.1ubuntu1 libselinux1_2.6-3build1 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.29-1ubuntu2 libsqlite3-0_3.16.2-3 libss2_1.43.4-2 libssl1.0.0_1.0.2g-1ubuntu12 libstdc++-6-dev_6.3.0-17ubuntu1 libstdc++6_7.1.0-4ubuntu1 libsystemd0_233-6ubuntu1 libtasn1-6_4.10-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libtsan0_7.1.0-4ubuntu1 libubsan0_7.1.0-4ubuntu1 libudev1_233-6ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-31 libustr-1.0-1_1.0.4-6 libuuid1_2.29-1ubuntu2 libwind0-heimdal_7.1.0+dfsg-13 libxml2_2.9.4+dfsg1-2.2build1 linux-libc-dev_4.10.0-21.23 lockfile-progs_0.1.17build1 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.29-1ubuntu2 multiarch-support_2.24-9ubuntu2 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu12 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1build1 perl_5.24.1-2ubuntu1 perl-base_5.24.1-2ubuntu1 perl-modules-5.24_5.24.1-2ubuntu1 pinentry-curses_1.0.0-2 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_1:1.12.1-1ubuntu2 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_3.5.3-1ubuntu3 python3-all_3.5.3-1ubuntu3 python3-all-dev_3.5.3-1ubuntu3 python3-dev_3.5.3-1ubuntu3 python3-minimal_3.5.3-1ubuntu3 python3-numpy_1:1.12.1-1ubuntu2 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 python3.6_3.6.1-1 python3.6-dev_3.6.1-1 python3.6-minimal_3.6.1-1 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=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 amd64 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-amd64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:184: python3.6 setup.py clean WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/<>/.pybuild/pythonX.Y_3.6/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.6' 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-amd64' 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 dh build --with python2,python3 --buildsystem=pybuild dh_testdir -O--buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_auto_configure -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: python3.6 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 -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/python3.6 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/python3.6m 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/python3.6m -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 '/<>' 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 (1 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 (0 ms total) [----------] 2 tests from AffineAlignmentTests [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest [ OK ] AffineAlignmentTests.LargeGapTest (10 ms) [----------] 2 tests from AffineAlignmentTests (10 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 (1 ms) [----------] 1 test from LinearAlignmentTests (1 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 (2 ms) [ RUN ] RecursorTest/0.LinkTest [ OK ] RecursorTest/0.LinkTest (1 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 (3 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 (3 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 (0 ms) [----------] 7 tests from RecursorTest/1 (3 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 (2 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 (3 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 (2 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/3 (3 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (83 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (74 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (82 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (25 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (24 ms) [----------] 5 tests from RecursorFuzzTest/0 (289 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (55 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (58 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (58 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (25 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (26 ms) [----------] 5 tests from RecursorFuzzTest/1 (223 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (102 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (81 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (101 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (20 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (19 ms) [----------] 5 tests from RecursorFuzzTest/2 (325 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (71 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (102 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (68 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (19 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (20 ms) [----------] 5 tests from RecursorFuzzTest/3 (280 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 (7 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 (9 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 (8 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 (8 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (45 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (49 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (51 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (37 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (4 ms) [----------] 5 tests from QvEvaluatorTest (187 ms total) [----------] 4 tests from MutationEnumerationTest [ RUN ] MutationEnumerationTest.TestAllMutations [ OK ] MutationEnumerationTest.TestAllMutations (1 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 (1 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 (0 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 (5 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 (2 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 (0 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 (0 ms) [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning [ OK ] MutationScorerTest/3.MutationsAtBeginning (1 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (1 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 (1 ms) [----------] 1 test from QuiverConfigTableTests (1 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 (1 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (1 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 [ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest [ OK ] MultiReadMutationScorerTest/0.CopyTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (1 ms) [----------] 11 tests from MultiReadMutationScorerTest/0 (8 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (1 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 (1 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 (5 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (1 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (703 ms) [----------] 8 tests from PoaConsensus (712 ms total) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (2098 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 dh binary --with python2,python3 --buildsystem=pybuild create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -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/python3.6 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/python3.6m 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/python3.6m -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_3.6/build copying build/Python/_ConsensusCore.so -> /<>/.pybuild/pythonX.Y_3.6/build creating /<>/debian/python3-pbconsensuscore/usr creating /<>/debian/python3-pbconsensuscore/usr/lib creating /<>/debian/python3-pbconsensuscore/usr/lib/python3.6 creating /<>/debian/python3-pbconsensuscore/usr/lib/python3.6/dist-packages copying /<>/.pybuild/pythonX.Y_3.6/build/ConsensusCore.py -> /<>/debian/python3-pbconsensuscore/usr/lib/python3.6/dist-packages copying /<>/.pybuild/pythonX.Y_3.6/build/_ConsensusCore.so -> /<>/debian/python3-pbconsensuscore/usr/lib/python3.6/dist-packages byte-compiling /<>/debian/python3-pbconsensuscore/usr/lib/python3.6/dist-packages/ConsensusCore.py to ConsensusCore.cpython-36.pyc running install_egg_info running egg_info writing build/Python/ConsensusCore.egg-info/PKG-INFO writing dependency_links to build/Python/ConsensusCore.egg-info/dependency_links.txt writing top-level names to build/Python/ConsensusCore.egg-info/top_level.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/python3-pbconsensuscore/usr/lib/python3.6/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/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 build/Python/ConsensusCore.egg-info/PKG-INFO writing dependency_links to build/Python/ConsensusCore.egg-info/dependency_links.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/python3-pbconsensuscore/usr/lib/python3.5/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_python2 make[1]: Entering directory '/<>' dh_python2 I: dh_python2 fs:322: renaming _ConsensusCore.so to _ConsensusCore.x86_64-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-x86_64-linux-gnu.so I: dh_python3 fs:85: renaming debian/python3-pbconsensuscore/usr/lib/python3.6/dist-packages/_ConsensusCore.so to debian/python3-pbconsensuscore/usr/lib/python3.6/dist-packages/_ConsensusCore.cpython-36m-x86_64-linux-gnu.so dh_numpy3 make[1]: Leaving directory '/<>' dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild Normalizing debian/libconsensuscore-dev/usr/lib/x86_64-linux-gnu/libConsensusCore.a dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages/_ConsensusCore.x86_64-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-36m-x86_64-linux-gnu.so debian/python3-pbconsensuscore/usr/lib/python3/dist-packages/_ConsensusCore.cpython-35m-x86_64-linux-gnu.so were not linked against libpthread.so.0 (they use none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -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 ${python3:Depends} dpkg-gencontrol: warning: package libconsensuscore-dev: unused substitution variable ${python:Depends} dpkg-gencontrol: warning: package python-pbconsensuscore: 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 ${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 ${python: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} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python3:Versions} dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing libconsensuscore-dev (in debian/libconsensuscore-dev); do_strip: , oemstrip: pkgstriptranslations: processing python-pbconsensuscore-dbgsym (in debian/.debhelper/python-pbconsensuscore/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python3-pbconsensuscore-dbgsym (in debian/.debhelper/python3-pbconsensuscore/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libconsensuscore-dev/DEBIAN/control, package libconsensuscore-dev, directory debian/libconsensuscore-dev pkgstripfiles: processing control file: debian/.debhelper/python-pbconsensuscore/dbgsym-root/DEBIAN/control, package python-pbconsensuscore-dbgsym, directory debian/.debhelper/python-pbconsensuscore/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pbconsensuscore-dbgsym ... pkgstripfiles: No PNG files. pkgstripfiles: Running PNG optimization (using 4 cpus) for package libconsensuscore-dev ... dpkg-deb: building package 'python-pbconsensuscore-dbgsym' in 'debian/.debhelper/scratch-space/build-python-pbconsensuscore/python-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.deb'. pkgstripfiles: processing control file: debian/.debhelper/python3-pbconsensuscore/dbgsym-root/DEBIAN/control, package python3-pbconsensuscore-dbgsym, directory debian/.debhelper/python3-pbconsensuscore/dbgsym-root pkgstripfiles: No PNG files. pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pbconsensuscore-dbgsym ... dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.0.2-2build1_amd64.deb'. pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pbconsensuscore/python3-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.deb'. Renaming python-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.deb to python-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.ddeb Renaming python3-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.deb to python3-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.ddeb INFO: pkgstriptranslations version 131 pkgstriptranslations: processing python-pbconsensuscore (in debian/python-pbconsensuscore); do_strip: , oemstrip: INFO: pkgstriptranslations version 131 pkgstriptranslations: processing python3-pbconsensuscore (in debian/python3-pbconsensuscore); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python-pbconsensuscore/DEBIAN/control, package python-pbconsensuscore, directory debian/python-pbconsensuscore pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pbconsensuscore ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pbconsensuscore' in '../python-pbconsensuscore_1.0.2-2build1_amd64.deb'. pkgstripfiles: processing control file: debian/python3-pbconsensuscore/DEBIAN/control, package python3-pbconsensuscore, directory debian/python3-pbconsensuscore pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pbconsensuscore ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.0.2-2build1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../consensuscore_1.0.2-2build1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build consensuscore-1.0.2 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20170512-1127 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ consensuscore_1.0.2-2build1_amd64.changes: ------------------------------------------ Format: 1.8 Date: Fri, 12 May 2017 16:25:16 +0530 Source: consensuscore Binary: libconsensuscore-dev python-pbconsensuscore python3-pbconsensuscore Architecture: amd64 Version: 1.0.2-2build1 Distribution: artful-proposed 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: 9280a50558aee244b3a84850ec667ecb7dd6f3b8 8031 consensuscore_1.0.2-2build1_amd64.buildinfo 6379dac4bf0b86f101e994cfdaee1cda53907226 449398 libconsensuscore-dev_1.0.2-2build1_amd64.deb 22aca1f61019a12e40eede2dac106a4b985d3932 6267200 python-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.ddeb 13b65a98e2b45c77692ffff159fdea3d62e2f4a2 659916 python-pbconsensuscore_1.0.2-2build1_amd64.deb a71428ec0514af0972a273be15a2dd6927808e17 12546672 python3-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.ddeb 42d6878a9996a396d6a5e882609696bd5977d2ea 659440 python3-pbconsensuscore_1.0.2-2build1_amd64.deb Checksums-Sha256: 31a5de0cfde1d4ed7e2bd88d3b25505f55dde058d520a2763f882378060ae214 8031 consensuscore_1.0.2-2build1_amd64.buildinfo 5ba3da2f02a92cff859a5258d023018134bebf2cbd9e20ccf3555eb075d09fa7 449398 libconsensuscore-dev_1.0.2-2build1_amd64.deb 2ccf39fd235feea91ce8d41b1671321e20e710945174422e54f0a49f31869e32 6267200 python-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.ddeb 96afd543714663ea884ddcef251382480675cb9c12900e6c887695230d30e121 659916 python-pbconsensuscore_1.0.2-2build1_amd64.deb 974a27b21db3b13735d2f5483ecfe20250b2e07e30c994e55df08cd050afeb46 12546672 python3-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.ddeb 96d9d49cf5d1bfc9d66af5c2db4a932fd5e3e0e715f0fd4e4c24d3352b4519e4 659440 python3-pbconsensuscore_1.0.2-2build1_amd64.deb Files: 739f046539c14895c95e201ea07b4f3d 8031 science optional consensuscore_1.0.2-2build1_amd64.buildinfo bc99817e69abe25194967d4d58bc7f9c 449398 libdevel optional libconsensuscore-dev_1.0.2-2build1_amd64.deb d83056ffb1f3d751b76191162e6bc5fb 6267200 debug extra python-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.ddeb 9ecefd368bf1f34331fcf3774ae10b72 659916 python optional python-pbconsensuscore_1.0.2-2build1_amd64.deb abf328afd611648120066152b522d3f2 12546672 debug extra python3-pbconsensuscore-dbgsym_1.0.2-2build1_amd64.ddeb 65edf4b0ff0b37e51bc12b799c1f04ab 659440 python optional python3-pbconsensuscore_1.0.2-2build1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libconsensuscore-dev_1.0.2-2build1_amd64.deb -------------------------------------------- new debian package, version 2.0. size 449398 bytes: control archive=2217 bytes. 814 bytes, 18 lines control 4239 bytes, 52 lines md5sums Package: libconsensuscore-dev Source: consensuscore Version: 1.0.2-2build1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3676 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 2016-05-06 17:25 ./usr/include/ConsensusCore/Edna/EdnaConfig.hpp -rw-r--r-- root/root 2380 2016-05-06 17:25 ./usr/include/ConsensusCore/Edna/EdnaCounts.hpp -rw-r--r-- root/root 9283 2016-05-06 17:25 ./usr/include/ConsensusCore/Edna/EdnaEvaluator.hpp -rw-r--r-- root/root 5127 2016-05-06 17:25 ./usr/include/ConsensusCore/Feature.hpp -rw-r--r-- root/root 4278 2016-05-06 17:25 ./usr/include/ConsensusCore/Features.hpp -rw-r--r-- root/root 3563 2016-05-06 17:25 ./usr/include/ConsensusCore/Interval.hpp -rw-r--r-- root/root 2724 2016-05-06 17:25 ./usr/include/ConsensusCore/LFloat.hpp -rw-r--r-- root/root 2325 2016-05-06 17:25 ./usr/include/ConsensusCore/Logging.hpp drwxr-xr-x root/root 0 2016-05-06 17:25 ./usr/include/ConsensusCore/Matrix/ -rw-r--r-- root/root 2379 2016-05-06 17:25 ./usr/include/ConsensusCore/Matrix/AbstractMatrix.hpp -rw-r--r-- root/root 5120 2016-05-06 17:25 ./usr/include/ConsensusCore/Matrix/DenseMatrix-inl.hpp -rw-r--r-- root/root 4515 2016-05-06 17:25 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./usr/share/doc/libconsensuscore-dev/copyright python-pbconsensuscore_1.0.2-2build1_amd64.deb ---------------------------------------------- new debian package, version 2.0. size 659916 bytes: control archive=1231 bytes. 988 bytes, 19 lines control 685 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: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2941 Depends: libc6 (>= 2.14), 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. 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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 2976336 2017-05-12 10:55 ./usr/lib/python3/dist-packages/_ConsensusCore.cpython-35m-x86_64-linux-gnu.so -rw-r--r-- root/root 2976336 2017-05-12 10:55 ./usr/lib/python3/dist-packages/_ConsensusCore.cpython-36m-x86_64-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: amd64 Build-Space: 284964 Build-Time: 804 Distribution: artful-proposed Host Architecture: amd64 Install-Time: 58 Job: consensuscore_1.0.2-2build1.dsc Machine Architecture: amd64 Package: consensuscore Package-Time: 864 Source-Version: 1.0.2-2build1 Space: 284964 Status: successful Version: 1.0.2-2build1 -------------------------------------------------------------------------------- Finished at 20170512-1127 Build needed 00:14:24, 284964k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-12573736'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-12573736/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-12573736'] Unmounting chroot for build PACKAGEBUILD-12573736... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-12573736'] Removing build PACKAGEBUILD-12573736