https://launchpad.net/ubuntu/+source/consensuscore/1.0.2-3build1/+build/15604559 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-057 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.5 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 3 Nov 13:09:53 ntpdate[1805]: adjust time server 10.211.37.1 offset 0.083733 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15604559 /home/buildd/filecache-default/727e394105280e93a16c79dcca0079cc298d61c4 Creating target for build PACKAGEBUILD-15604559 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15604559 Starting target for build PACKAGEBUILD-15604559 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15604559 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15604559 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15604559 Updating target for build PACKAGEBUILD-15604559 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 Packages [1007 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe i386 Packages [8732 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5057 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main i386 Packages [76.9 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [46.6 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 Packages [328 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [202 kB] Fetched 16.4 MB in 7s (2374 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libgdbm6 libperl5.28 perl-modules-5.28 The following packages will be upgraded: base-files binutils binutils-common binutils-i686-linux-gnu cpp cpp-8 dmsetup g++ g++-8 gcc gcc-8 gcc-8-base libapparmor1 libasan5 libatomic1 libaudit-common libaudit1 libbinutils libcap-ng0 libcc1-0 libdevmapper1.02.1 libgcc-8-dev libgcc1 libgdbm-compat4 libgomp1 libitm1 libkmod2 libmpx2 libquadmath0 libseccomp2 libselinux1 libstdc++-8-dev libstdc++6 libubsan1 linux-libc-dev perl perl-base tzdata 38 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 42.1 MB of archives. After this operation, 42.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main i386 base-files i386 10.1ubuntu8 [60.2 kB] Get:2 http://ftpmaster.internal/ubuntu disco-proposed/main i386 perl-modules-5.28 all 5.28.0-3 [2818 kB] Get:3 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libgdbm6 i386 1.18.1-1 [32.1 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libgdbm-compat4 i386 1.18.1-1 [6704 B] Get:5 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libperl5.28 i386 5.28.0-3 [3436 kB] Get:6 http://ftpmaster.internal/ubuntu disco-proposed/main i386 perl i386 5.28.0-3 [204 kB] Get:7 http://ftpmaster.internal/ubuntu disco-proposed/main i386 perl-base i386 5.28.0-3 [1600 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main i386 libquadmath0 i386 8.2.0-9ubuntu1 [208 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main i386 libubsan1 i386 8.2.0-9ubuntu1 [138 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main i386 libitm1 i386 8.2.0-9ubuntu1 [30.8 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main i386 libasan5 i386 8.2.0-9ubuntu1 [375 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main i386 gcc-8-base i386 8.2.0-9ubuntu1 [18.6 kB] Get:13 http://ftpmaster.internal/ubuntu disco/main i386 libstdc++6 i386 8.2.0-9ubuntu1 [430 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main i386 libgomp1 i386 8.2.0-9ubuntu1 [80.7 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main i386 libatomic1 i386 8.2.0-9ubuntu1 [9604 B] Get:16 http://ftpmaster.internal/ubuntu disco/main i386 libmpx2 i386 8.2.0-9ubuntu1 [13.0 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main i386 cpp-8 i386 8.2.0-9ubuntu1 [7537 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main i386 libcc1-0 i386 8.2.0-9ubuntu1 [41.9 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main i386 gcc-8 i386 8.2.0-9ubuntu1 [8330 kB] Get:20 http://ftpmaster.internal/ubuntu disco/main i386 g++-8 i386 8.2.0-9ubuntu1 [8444 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main i386 libstdc++-8-dev i386 8.2.0-9ubuntu1 [1586 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main i386 libgcc-8-dev i386 8.2.0-9ubuntu1 [2299 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main i386 libgcc1 i386 1:8.2.0-9ubuntu1 [48.1 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main i386 libbinutils i386 2.31.1-7ubuntu1 [518 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main i386 binutils-common i386 2.31.1-7ubuntu1 [194 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main i386 binutils i386 2.31.1-7ubuntu1 [3392 B] Get:27 http://ftpmaster.internal/ubuntu disco/main i386 binutils-i686-linux-gnu i386 2.31.1-7ubuntu1 [1985 kB] Get:28 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:29 http://ftpmaster.internal/ubuntu disco/main i386 libcap-ng0 i386 0.7.9-1build1 [11.1 kB] Get:30 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libaudit1 i386 1:2.8.3-1ubuntu3 [40.0 kB] Get:31 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libselinux1 i386 2.8-1build2 [73.5 kB] Get:32 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libseccomp2 i386 2.3.3-3ubuntu2 [35.6 kB] Get:33 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libdevmapper1.02.1 i386 2:1.02.145-4.1ubuntu4 [125 kB] Get:34 http://ftpmaster.internal/ubuntu disco-proposed/main i386 dmsetup i386 2:1.02.145-4.1ubuntu4 [70.4 kB] Get:35 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libapparmor1 i386 2.12-4ubuntu10 [31.3 kB] Get:36 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libkmod2 i386 25-1ubuntu1.1 [47.7 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main i386 tzdata all 2018g-1 [188 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main i386 g++ i386 4:8.2.0-2ubuntu2 [1616 B] Get:39 http://ftpmaster.internal/ubuntu disco/main i386 gcc i386 4:8.2.0-2ubuntu2 [5272 B] Get:40 http://ftpmaster.internal/ubuntu disco/main i386 cpp i386 4:8.2.0-2ubuntu2 [27.6 kB] Get:41 http://ftpmaster.internal/ubuntu disco-proposed/main i386 linux-libc-dev i386 4.18.0-11.12 [1040 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 42.1 MB in 9s (4814 kB/s) (Reading database ... 12644 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu8_i386.deb ... Unpacking base-files (10.1ubuntu8) over (10.1ubuntu7) ... Setting up base-files (10.1ubuntu8) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 12644 files and directories currently installed.) Preparing to unpack .../0-perl_5.28.0-3_i386.deb ... Unpacking perl (5.28.0-3) over (5.26.2-7) ... Selecting previously unselected package perl-modules-5.28. Preparing to unpack .../1-perl-modules-5.28_5.28.0-3_all.deb ... Unpacking perl-modules-5.28 (5.28.0-3) ... Selecting previously unselected package libgdbm6:i386. Preparing to unpack .../2-libgdbm6_1.18.1-1_i386.deb ... Unpacking libgdbm6:i386 (1.18.1-1) ... Preparing to unpack .../3-libgdbm-compat4_1.18.1-1_i386.deb ... Unpacking libgdbm-compat4:i386 (1.18.1-1) over (1.14.1-6) ... Selecting previously unselected package libperl5.28:i386. 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Unpacking linux-libc-dev:i386 (4.18.0-11.12) over (4.18.0-10.11) ... Setting up libquadmath0:i386 (8.2.0-9ubuntu1) ... Setting up cpp-8 (8.2.0-9ubuntu1) ... Setting up libgomp1:i386 (8.2.0-9ubuntu1) ... Setting up libatomic1:i386 (8.2.0-9ubuntu1) ... Setting up cpp (4:8.2.0-2ubuntu2) ... Setting up libcc1-0:i386 (8.2.0-9ubuntu1) ... Setting up tzdata (2018g-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Nov 3 13:10:44 UTC 2018. Universal Time is now: Sat Nov 3 13:10:44 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up linux-libc-dev:i386 (4.18.0-11.12) ... Setting up libdevmapper1.02.1:i386 (2:1.02.145-4.1ubuntu4) ... Setting up libkmod2:i386 (25-1ubuntu1.1) ... Setting up libgdbm6:i386 (1.18.1-1) ... Setting up binutils-common:i386 (2.31.1-7ubuntu1) ... Setting up libmpx2:i386 (8.2.0-9ubuntu1) ... Setting up perl-modules-5.28 (5.28.0-3) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up libapparmor1:i386 (2.12-4ubuntu10) ... Setting up dmsetup (2:1.02.145-4.1ubuntu4) ... Setting up libgdbm-compat4:i386 (1.18.1-1) ... Setting up libasan5:i386 (8.2.0-9ubuntu1) ... Setting up libitm1:i386 (8.2.0-9ubuntu1) ... Setting up libubsan1:i386 (8.2.0-9ubuntu1) ... Setting up libbinutils:i386 (2.31.1-7ubuntu1) ... Setting up libperl5.28:i386 (5.28.0-3) ... Setting up perl (5.28.0-3) ... Setting up binutils-i686-linux-gnu (2.31.1-7ubuntu1) ... Setting up libgcc-8-dev:i386 (8.2.0-9ubuntu1) ... Setting up binutils (2.31.1-7ubuntu1) ... Setting up libstdc++-8-dev:i386 (8.2.0-9ubuntu1) ... Setting up gcc-8 (8.2.0-9ubuntu1) ... Setting up g++-8 (8.2.0-9ubuntu1) ... Setting up gcc (4:8.2.0-2ubuntu2) ... Setting up g++ (4:8.2.0-2ubuntu2) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15604559 i386 disco-proposed -c chroot:build-PACKAGEBUILD-15604559 --arch=i386 --dist=disco-proposed --nolog consensuscore_1.0.2-3build1.dsc Initiating build PACKAGEBUILD-15604559 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-057.buildd +==============================================================================+ | consensuscore 1.0.2-3build1 (i386) 03 Nov 2018 13:10 | +==============================================================================+ Package: consensuscore Version: 1.0.2-3build1 Source Version: 1.0.2-3build1 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/consensuscore-Ys45rJ/consensuscore-1.0.2' with '<>' I: NOTICE: Log filtering will replace 'build/consensuscore-Ys45rJ' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15604559/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- consensuscore_1.0.2-3build1.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-21cxT_/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-21cxT_/apt_archive ./ InRelease Get:2 copy:/<>/resolver-21cxT_/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-21cxT_/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-21cxT_/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-21cxT_/apt_archive ./ Packages [524 B] Fetched 2857 B in 0s (104 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 packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. 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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-21cxT_/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14533 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), 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 (>= 11~), 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-uH0giw/apt_archive/sbuild-build-depends-consensuscore-dummy.deb'. Ign:1 copy:/<>/resolver-uH0giw/apt_archive ./ InRelease Get:2 copy:/<>/resolver-uH0giw/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-uH0giw/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-uH0giw/apt_archive ./ Sources [274 B] Get:5 copy:/<>/resolver-uH0giw/apt_archive ./ Packages [594 B] Fetched 2987 B in 0s (117 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 packages were automatically installed and are no longer required: libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libboost-dev libboost1.67-dev libbsd0 libcroco3 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libicu60 liblapack3 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-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 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-distutils python3-lib2to3 python3-minimal python3-numpy python3-pkg-resources python3-setuptools python3.7 python3.7-dev python3.7-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 libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev libboost-coroutine1.67-dev libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev libboost-filesystem1.67-dev libboost-graph1.67-dev libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev libboost-program-options1.67-dev libboost-python1.67-dev libboost-random1.67-dev libboost-regex1.67-dev libboost-serialization1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk gfortran python-nose python-numpy-dbg python-numpy-doc python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3-nose python3-numpy-dbg python3.7-venv python3.7-doc swig-doc swig-examples swig3.0-examples swig3.0-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libboost-dev libboost1.67-dev libbsd0 libcroco3 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libicu60 liblapack3 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-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 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-dev python3-distutils python3-lib2to3 python3-minimal python3-numpy python3-pkg-resources python3-setuptools python3.7 python3.7-dev python3.7-minimal sbuild-build-depends-consensuscore-dummy swig swig3.0 0 upgraded, 88 newly installed, 0 to remove and 0 not upgraded. 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Setting up libxml2:i386 (2.9.4+dfsg1-7ubuntu2) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libmagic1:i386 (1:5.34-2) ... Setting up libcroco3:i386 (0.6.12-2) ... Setting up libblas3:i386 (3.8.0-1build1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up libboost1.67-dev:i386 (1.67.0-8) ... Setting up libexpat1-dev:i386 (2.2.6-1) ... Setting up libboost-dev:i386 (1.67.0.0ubuntu1) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 libgfortran5:i386 (8.2.0-9ubuntu1) ... Setting up libpython2.7-stdlib:i386 (2.7.15-4ubuntu4) ... Setting up autopoint (0.19.8.1-8) ... Setting up libmpdec2:i386 (2.4.2-2) ... Setting up libfile-stripnondeterminism-perl (0.042-1) ... Setting up swig (3.0.12-1.2) ... Setting up libpython3.7-stdlib:i386 (3.7.1-1) ... Setting up gettext (0.19.8.1-8) ... Setting up liblapack3:i386 (3.8.0-1build1) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up python2.7 (2.7.15-4ubuntu4) ... Setting up python3.7 (3.7.1-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libpython3.7:i386 (3.7.1-1) ... Setting up libpython2.7:i386 (2.7.15-4ubuntu4) ... Setting up automake (1:1.16.1-3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.7-dev:i386 (3.7.1-1) ... Setting up man-db (2.8.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2-stdlib:i386 (2.7.15-3) ... Setting up libpython2.7-dev:i386 (2.7.15-4ubuntu4) ... Setting up python2.7-dev (2.7.15-4ubuntu4) ... Setting up libpython3-dev:i386 (3.7.1-1ubuntu1) ... Setting up libtool (2.4.6-4) ... Setting up libpython3-stdlib:i386 (3.7.1-1ubuntu1) ... Setting up po-debconf (1.0.20) ... Setting up python3 (3.7.1-1ubuntu1) ... Setting up python3-numpy (1:1.14.5-1ubuntu7) ... Setting up python3-pkg-resources (40.2.0-1) ... Setting up python3.7-dev (3.7.1-1) ... Setting up python2 (2.7.15-3) ... Setting up libpython2-dev:i386 (2.7.15-3) ... Setting up libpython-stdlib:i386 (2.7.15-3) ... Setting up libpython3-all-dev:i386 (3.7.1-1ubuntu1) ... Setting up python2-dev (2.7.15-3) ... Setting up python3-lib2to3 (3.7.1-1) ... Setting up python3-distutils (3.7.1-1) ... Setting up python (2.7.15-3) ... Setting up libpython-dev:i386 (2.7.15-3) ... Setting up python-dev (2.7.15-3) ... Setting up libpython-all-dev:i386 (2.7.15-3) ... Setting up python-pkg-resources (40.2.0-1) ... Setting up python-numpy (1:1.14.5-1ubuntu7) ... Setting up python3-setuptools (40.2.0-1) ... Setting up dh-python (3.20180927ubuntu1) ... Setting up python-all (2.7.15-3) ... Setting up python-setuptools (40.2.0-1) ... Setting up python3-dev (3.7.1-1ubuntu1) ... Setting up python-all-dev (2.7.15-3) ... Setting up python3-all (3.7.1-1ubuntu1) ... Setting up python3-all-dev (3.7.1-1ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (0.042-1) ... Setting up debhelper (11.3.2ubuntu1) ... Setting up dh-exec (0.23build1) ... Setting up sbuild-build-depends-consensuscore-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-138-generic amd64 (i686) Toolchain package versions: binutils_2.31.1-7ubuntu1 dpkg-dev_1.19.0.5ubuntu5 g++-8_8.2.0-9ubuntu1 gcc-8_8.2.0-9ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 linux-libc-dev_4.18.0-11.12 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-3 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-7ubuntu1 binutils-common_2.31.1-7ubuntu1 binutils-i686-linux-gnu_2.31.1-7ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bzip2_1.0.6-9 ca-certificates_20180409 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-9ubuntu1 dash_0.5.8-2.10 debconf_1.5.69 debhelper_11.3.2ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-exec_0.23build1 dh-python_3.20180927ubuntu1 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.0.5ubuntu5 dpkg-dev_1.19.0.5ubuntu5 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 fakeroot_1.22-2ubuntu1 fdisk_2.32-0.1ubuntu2 file_1:5.34-2 findutils_4.6.0+git+20180808-2 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-9ubuntu1 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-9ubuntu1 gcc-8-base_8.2.0-9ubuntu1 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gpg_2.2.8-3ubuntu1 gpg-agent_2.2.8-3ubuntu1 gpgconf_2.2.8-3ubuntu1 gpgv_2.2.8-3ubuntu1 grep_3.1-2ubuntu1 groff-base_1.22.3-10 gzip_1.6-5ubuntu2 hostname_3.20 init_1.54 init-system-helpers_1.54 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.63-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-9ubuntu1 libassuan0_2.5.1-2 libatomic1_8.2.0-9ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbinutils_2.31.1-7ubuntu1 libblas3_3.8.0-1build1 libblkid1_2.32-0.1ubuntu2 libboost-dev_1.67.0.0ubuntu1 libboost1.67-dev_1.67.0-8 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-1build1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-9ubuntu1 libcom-err2_1.44.4-2 libcomerr2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2ubuntu2 libdb5.3_5.3.28+dfsg1-0.1 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.0.5ubuntu5 libelf1_0.170-0.5.0ubuntu1 libexpat1_2.2.6-1 libexpat1-dev_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.22-2ubuntu1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libgcc-8-dev_8.2.0-9ubuntu1 libgcc1_1:8.2.0-9ubuntu1 libgcrypt20_1.8.3-1ubuntu1 libgdbm-compat4_1.18.1-1 libgdbm5_1.14.1-6 libgdbm6_1.18.1-1 libgfortran5_8.2.0-9ubuntu1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.6.4-2ubuntu1 libgomp1_8.2.0-9ubuntu1 libgpg-error0_1.32-1 libhogweed4_3.4-1 libicu60_60.2-6ubuntu1 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu2 libisl19_0.20-2 libitm1_8.2.0-9ubuntu1 libjson-c3_0.12.1-1.3 libkmod2_25-1ubuntu1.1 liblapack3_3.8.0-1build1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libmpx2_8.2.0-9ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4-1 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libperl5.26_5.26.2-7 libperl5.28_5.28.0-3 libpipeline1_1.5.0-1 libpng16-16_1.6.34-2 libprocps7_2:3.3.15-2ubuntu1 libpython-all-dev_2.7.15-3 libpython-dev_2.7.15-3 libpython-stdlib_2.7.15-3 libpython2-dev_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7_2.7.15-4ubuntu4 libpython2.7-dev_2.7.15-4ubuntu4 libpython2.7-minimal_2.7.15-4ubuntu4 libpython2.7-stdlib_2.7.15-4ubuntu4 libpython3-all-dev_3.7.1-1ubuntu1 libpython3-dev_3.7.1-1ubuntu1 libpython3-stdlib_3.7.1-1ubuntu1 libpython3.7_3.7.1-1 libpython3.7-dev_3.7.1-1 libpython3.7-minimal_3.7.1-1 libpython3.7-stdlib_3.7.1-1 libquadmath0_8.2.0-9ubuntu1 libreadline7_7.0-5 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-1build1 libsemanage1_2.8-1build1 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu2 libsqlite3-0_3.24.0-1 libss2_1.44.4-2 libssl1.1_1.1.1-1ubuntu2 libstdc++-8-dev_8.2.0-9ubuntu1 libstdc++6_8.2.0-9ubuntu1 libsystemd0_239-7ubuntu10 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-4 libubsan1_8.2.0-9ubuntu1 libudev1_239-7ubuntu10 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu2 libxml2_2.9.4+dfsg1-7ubuntu2 libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.18.0-11.12 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1ubuntu1 make_4.2.1-1.2 man-db_2.8.4-2 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.0-3 perl-base_5.28.0-3 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.0-3 pinentry-curses_1.1.0-1build2 pkgbinarymangler_143 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python_2.7.15-3 python-all_2.7.15-3 python-all-dev_2.7.15-3 python-dev_2.7.15-3 python-minimal_2.7.15-3 python-numpy_1:1.14.5-1ubuntu7 python-pkg-resources_40.2.0-1 python-setuptools_40.2.0-1 python2_2.7.15-3 python2-dev_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-4ubuntu4 python2.7-dev_2.7.15-4ubuntu4 python2.7-minimal_2.7.15-4ubuntu4 python3_3.7.1-1ubuntu1 python3-all_3.7.1-1ubuntu1 python3-all-dev_3.7.1-1ubuntu1 python3-dev_3.7.1-1ubuntu1 python3-distutils_3.7.1-1 python3-lib2to3_3.7.1-1 python3-minimal_3.7.1-1ubuntu1 python3-numpy_1:1.14.5-1ubuntu7 python3-pkg-resources_40.2.0-1 python3-setuptools_40.2.0-1 python3.7_3.7.1-1 python3.7-dev_3.7.1-1 python3.7-minimal_3.7.1-1 readline-common_7.0-5 sbuild-build-depends-consensuscore-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 swig_3.0.12-1.2 swig3.0_3.0.12-1.2 systemd_239-7ubuntu10 systemd-sysv_239-7ubuntu10 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-2 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 util-linux_2.32-0.1ubuntu2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Nov 3 12:20:53 2018 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./consensuscore_1.0.2-3build1.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_1.0.2-3build1.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=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15604559 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15604559 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15604559 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.0.2-3build1 dpkg-buildpackage: info: source distribution disco dpkg-source --before-build consensuscore-1.0.2 dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --with python2,python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py clean WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/<>/.pybuild/cpython2_2.7_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/<>/.pybuild/cpython3_3.7_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python2,python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:217: 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:217: python3.7 setup.py config WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:217: /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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /<>/build/C++/MutationScorer.o src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:253:20: required from here src/C++/Quiver/MutationScorer.cpp:71:9: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] catch(AlphaBetaMismatchException e) { ^~~~~ src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:254:20: required from here src/C++/Quiver/MutationScorer.cpp:71:9: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:255:20: required from here src/C++/Quiver/MutationScorer.cpp:71:9: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:256:20: required from here src/C++/Quiver/MutationScorer.cpp:71:9: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:257:20: required from here src/C++/Quiver/MutationScorer.cpp:71:9: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:258:20: required from here src/C++/Quiver/MutationScorer.cpp:71:9: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SseRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::EdnaEvaluator]’: src/C++/Quiver/MutationScorer.cpp:259:20: required from here src/C++/Quiver/MutationScorer.cpp:71:9: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -MT /<>/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /<>/build/C++/LinearAlignment.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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -MT /<>/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /<>/build/C++/Checksum.d ar crs /<>/build/C++/libConsensusCore.a /<>/build/C++/Binomial.o /<>/build/C++/Features.o /<>/build/C++/Logging.o /<>/build/C++/ReadScorer.o /<>/build/C++/MultiReadMutationScorer.o /<>/build/C++/MutationEnumerator.o /<>/build/C++/QuiverConfig.o /<>/build/C++/Diploid.o /<>/build/C++/MutationScorer.o /<>/build/C++/SseRecursor.o /<>/build/C++/QuiverConsensus.o /<>/build/C++/RecursorBase.o /<>/build/C++/SimpleRecursor.o /<>/build/C++/Mutation.o /<>/build/C++/Sequence.o /<>/build/C++/EdnaCounts.o /<>/build/C++/Utils.o /<>/build/C++/SparseMatrix.o /<>/build/C++/DenseMatrix.o /<>/build/C++/Read.o /<>/build/C++/Coverage.o /<>/build/C++/PairwiseAlignment.o /<>/build/C++/AffineAlignment.o /<>/build/C++/AlignConfig.o /<>/build/C++/LinearAlignment.o /<>/build/C++/Version.o /<>/build/C++/Feature.o /<>/build/C++/PoaGraphImpl.o /<>/build/C++/PoaGraphTraversals.o /<>/build/C++/PoaConsensus.o /<>/build/C++/RangeFinder.o /<>/build/C++/PoaGraph.o /<>/build/C++/Checksum.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 -Wl,-z,now -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 In file included from /<>/include/ConsensusCore/Quiver/QvEvaluator.hpp:54, from /<>/build/Python/ConsensusCore_wrap.cxx:6764: /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:230:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool Insert(const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:237:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool InsertAs(const std::string& name, const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:241:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const QuiverConfig& At(const std::string& name) const throw(InvalidInputError); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/SimpleRecursor.hpp:43, from /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:46, from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/build/Python/ConsensusCore_wrap.cxx:7581: /<>/include/ConsensusCore/Quiver/detail/RecursorBase.hpp:79:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/build/Python/ConsensusCore_wrap.cxx:7581: /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:63:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:71:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/build/Python/ConsensusCore_wrap.cxx:7586: /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:58:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:62:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:66:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:70:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' I: pybuild base:217: /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/python3.7m 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 -Wl,-z,now -pthread -shared -Wl,-O1 -I/<>/include -I/<>/external -I /usr/include/python3.7m -I /usr/lib/python3/dist-packages/numpy/core/include /<>/build/Python/ConsensusCore_wrap.cxx /<>/build/C++/libConsensusCore.a -o /<>/build/Python/_ConsensusCore.so In file included from /<>/include/ConsensusCore/Quiver/QvEvaluator.hpp:54, from /<>/build/Python/ConsensusCore_wrap.cxx:6764: /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:230:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool Insert(const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:237:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool InsertAs(const std::string& name, const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:241:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const QuiverConfig& At(const std::string& name) const throw(InvalidInputError); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/SimpleRecursor.hpp:43, from /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:46, from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/build/Python/ConsensusCore_wrap.cxx:7581: /<>/include/ConsensusCore/Quiver/detail/RecursorBase.hpp:79:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/build/Python/ConsensusCore_wrap.cxx:7581: /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:63:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:71:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/build/Python/ConsensusCore_wrap.cxx:7586: /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:58:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:62:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:66:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:70:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ 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 -Wl,-z,now -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestMultiReadMutationScorer.cpp -o /<>/build/Tests/TestMultiReadMutationScorer.o In file included from /<>/include/ConsensusCore/Quiver/QvEvaluator.hpp:54, from /<>/include/ConsensusCore/Quiver/SimpleRecursor.hpp:41, from /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:46, from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/src/Tests/TestMultiReadMutationScorer.cpp:43: /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:230:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool Insert(const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:237:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool InsertAs(const std::string& name, const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:241:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const QuiverConfig& At(const std::string& name) const throw(InvalidInputError); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/SimpleRecursor.hpp:43, from /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:46, from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/src/Tests/TestMultiReadMutationScorer.cpp:43: /<>/include/ConsensusCore/Quiver/detail/RecursorBase.hpp:79:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/src/Tests/TestMultiReadMutationScorer.cpp:43: /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:63:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:71:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/src/Tests/TestMultiReadMutationScorer.cpp:45: /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:58:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:62:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:66:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:70:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ 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 -Wl,-z,now -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 -Wl,-z,now -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestMutationScorer.cpp -o /<>/build/Tests/TestMutationScorer.o In file included from /<>/include/ConsensusCore/Quiver/QvEvaluator.hpp:54, from /<>/include/ConsensusCore/Quiver/SimpleRecursor.hpp:41, from /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:46, from /<>/src/Tests/TestMutationScorer.cpp:47: /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:230:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool Insert(const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:237:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool InsertAs(const std::string& name, const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:241:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const QuiverConfig& At(const std::string& name) const throw(InvalidInputError); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/SimpleRecursor.hpp:43, from /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:46, from /<>/src/Tests/TestMutationScorer.cpp:47: /<>/include/ConsensusCore/Quiver/detail/RecursorBase.hpp:79:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/src/Tests/TestMutationScorer.cpp:47: /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:63:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:71:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/src/Tests/TestMutationScorer.cpp:50: /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:58:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:62:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:66:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:70:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ 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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/ParameterSettings.cpp -o /<>/build/Tests/ParameterSettings.o In file included from /<>/src/Tests/ParameterSettings.cpp:40: /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:230:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool Insert(const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:237:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool InsertAs(const std::string& name, const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:241:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const QuiverConfig& At(const std::string& name) const throw(InvalidInputError); ^~~~~ 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 -Wl,-z,now -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 -Wl,-z,now -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestQvEvaluator.cpp -o /<>/build/Tests/TestQvEvaluator.o In file included from /<>/include/ConsensusCore/Quiver/QvEvaluator.hpp:54, from /<>/src/Tests/TestQvEvaluator.cpp:46: /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:230:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool Insert(const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:237:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool InsertAs(const std::string& name, const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:241:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const QuiverConfig& At(const std::string& name) const throw(InvalidInputError); ^~~~~ In file included from /<>/src/Tests/TestQvEvaluator.cpp:50: /<>/src/Tests/Random.hpp: In function ‘std::vector RandomSampleWithoutReplacement(RNG&, int, int)’: /<>/src/Tests/Random.hpp:162:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ 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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now -I/<>/external/gmock-1.7.0 -c /<>/src/Tests/TestRecursors.cpp -o /<>/build/Tests/TestRecursors.o In file included from /<>/include/ConsensusCore/Quiver/QvEvaluator.hpp:54, from /<>/src/Tests/TestRecursors.cpp:48: /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:230:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool Insert(const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:237:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool InsertAs(const std::string& name, const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:241:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const QuiverConfig& At(const std::string& name) const throw(InvalidInputError); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/SimpleRecursor.hpp:43, from /<>/src/Tests/TestRecursors.cpp:50: /<>/include/ConsensusCore/Quiver/detail/RecursorBase.hpp:79:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/src/Tests/TestRecursors.cpp:56: /<>/src/Tests/Random.hpp: In function ‘std::vector RandomSampleWithoutReplacement(RNG&, int, int)’: /<>/src/Tests/Random.hpp:162:1: warning: no return statement in function returning non-void [-Wreturn-type] } ^ 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 -Wl,-z,now -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 -Wl,-z,now -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 -Wl,-z,now /<>/build/Tests/TestMultiReadMutationScorer.o /<>/build/Tests/TestPairwiseAlignment.o /<>/build/Tests/TestMutationScorer.o /<>/build/Tests/TestDiploidQuiver.o /<>/build/Tests/TestMutationEnumerator.o /<>/build/Tests/ParameterSettings.o /<>/build/Tests/TestMatrixFacades.o /<>/build/Tests/TestQvEvaluator.o /<>/build/Tests/TestMutations.o /<>/build/Tests/TestCoverage.o /<>/build/Tests/TestRecursors.o /<>/build/Tests/TestSparseVector.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. [----------] 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 (3 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest [ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (7 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest [ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (3 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (1 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 [ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (3 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest [ OK ] MultiReadMutationScorerTest/0.CopyTest (2 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (1 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (1 ms) [----------] 11 tests from MultiReadMutationScorerTest/0 (22 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 (1 ms) [----------] 3 tests from PairwiseAlignmentTests (1 ms total) [----------] 2 tests from AffineAlignmentTests [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest [ OK ] AffineAlignmentTests.LargeGapTest (26 ms) [----------] 2 tests from AffineAlignmentTests (26 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) [----------] 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 (7 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (5 ms) [----------] 8 tests from MutationScorerTest/0 (13 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 (1 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 (8 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (4 ms) [----------] 8 tests from MutationScorerTest/1 (14 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest [ OK ] MutationScorerTest/2.BasicTest (1 ms) [ RUN ] MutationScorerTest/2.CopyTest [ OK ] MutationScorerTest/2.CopyTest (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtBeginning [ OK ] MutationScorerTest/2.MutationsAtBeginning (1 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 (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (8 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (4 ms) [----------] 8 tests from MutationScorerTest/2 (15 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest [ OK ] MutationScorerTest/3.BasicTest (1 ms) [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning [ OK ] MutationScorerTest/3.MutationsAtBeginning (1 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (1 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (1 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest [ OK ] MutationScorerTest/3.DinucleotideInsertionTest (7 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest [ OK ] MutationScorerTest/3.DinucleotideDeletionTest (5 ms) [----------] 8 tests from MutationScorerTest/3 (16 ms total) [----------] 4 tests from MutationEnumerationTest [ RUN ] MutationEnumerationTest.TestAllMutations [ OK ] MutationEnumerationTest.TestAllMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueMutations [ OK ] MutationEnumerationTest.TestUniqueMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations [ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (9 ms) [ RUN ] MutationEnumerationTest.TestDinucleotideMutations [ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) [----------] 4 tests from MutationEnumerationTest (9 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 (1 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 (34 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 (35 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 (24 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 (24 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (311 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (343 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (411 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (251 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (21 ms) [----------] 5 tests from QvEvaluatorTest (1337 ms total) [----------] 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 (1 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 CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (2 ms) [ RUN ] CoverageTests.CoveredIntervalsTest2 [ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) [----------] 3 tests from CoverageTests (2 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 (3 ms) [ RUN ] RecursorTest/0.LinkTest [ OK ] RecursorTest/0.LinkTest (0 ms) [ RUN ] RecursorTest/0.ExtendAlphaTest [ OK ] RecursorTest/0.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/0.ExtendBetaTest [ OK ] RecursorTest/0.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/0 (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 (12 ms) [ RUN ] RecursorTest/1.LinkTest [ OK ] RecursorTest/1.LinkTest (1 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 (13 ms total) [----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/2.SmallMatchTest [ OK ] RecursorTest/2.SmallMatchTest (1 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 (11 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (0 ms) [ RUN ] RecursorTest/2.ExtendAlphaTest [ OK ] RecursorTest/2.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/2.ExtendBetaTest [ OK ] RecursorTest/2.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/2 (13 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 (1 ms) [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest [ OK ] RecursorTest/3.MediumSizedTest (11 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (1 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (1 ms) [----------] 7 tests from RecursorTest/3 (14 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (67 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (69 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (72 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (152 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (153 ms) [----------] 5 tests from RecursorFuzzTest/0 (513 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (267 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (267 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (259 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (147 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (149 ms) [----------] 5 tests from RecursorFuzzTest/1 (1089 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (357 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (358 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (371 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (121 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (123 ms) [----------] 5 tests from RecursorFuzzTest/2 (1330 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (296 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (291 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (300 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (117 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (119 ms) [----------] 5 tests from RecursorFuzzTest/3 (1126 ms total) [----------] 2 tests from SparseVectorTest [ RUN ] SparseVectorTest.BasicTest [ OK ] SparseVectorTest.BasicTest (0 ms) [ RUN ] SparseVectorTest.BasicTest2 [ OK ] SparseVectorTest.BasicTest2 (0 ms) [----------] 2 tests from SparseVectorTest (0 ms total) [----------] 1 test from SparseVector [ RUN ] SparseVector.CopyTest [ OK ] SparseVector.CopyTest (0 ms) [----------] 1 test from SparseVector (0 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest [ OK ] PoaGraph.SmallBasicTest (1 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (2 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (1 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (2 ms) [----------] 4 tests from PoaGraph (6 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (1 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (1 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) [ RUN ] PoaConsensus.SmallTilingTest [ OK ] PoaConsensus.SmallTilingTest (1 ms) [ RUN ] PoaConsensus.TestVerboseGraphVizOutput [ OK ] PoaConsensus.TestVerboseGraphVizOutput (1 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png sh: 1: dot: not found [ OK ] PoaConsensus.TestLocalStaggered (14 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (3 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (2084 ms) [----------] 8 tests from PoaConsensus (2106 ms total) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (7730 ms total) [ PASSED ] 158 tests. make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python2,python3 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:217: /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 -Wl,-z,now -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 In file included from /<>/include/ConsensusCore/Quiver/QvEvaluator.hpp:54, from /<>/build/Python/ConsensusCore_wrap.cxx:6764: /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:230:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool Insert(const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:237:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool InsertAs(const std::string& name, const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:241:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const QuiverConfig& At(const std::string& name) const throw(InvalidInputError); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/SimpleRecursor.hpp:43, from /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:46, from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/build/Python/ConsensusCore_wrap.cxx:7581: /<>/include/ConsensusCore/Quiver/detail/RecursorBase.hpp:79:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/build/Python/ConsensusCore_wrap.cxx:7581: /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:63:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:71:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/build/Python/ConsensusCore_wrap.cxx:7586: /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:58:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:62:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:66:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:70:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' running install running install_lib running build_py copying build/Python/ConsensusCore.py -> /<>/.pybuild/cpython2_2.7_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /<>/.pybuild/cpython2_2.7_pbconsensuscore/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/cpython2_2.7_pbconsensuscore/build/ConsensusCore.py -> /<>/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages copying /<>/.pybuild/cpython2_2.7_pbconsensuscore/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:217: /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/python3.7m 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 -Wl,-z,now -pthread -shared -Wl,-O1 -I/<>/include -I/<>/external -I /usr/include/python3.7m -I /usr/lib/python3/dist-packages/numpy/core/include /<>/build/Python/ConsensusCore_wrap.cxx /<>/build/C++/libConsensusCore.a -o /<>/build/Python/_ConsensusCore.so In file included from /<>/include/ConsensusCore/Quiver/QvEvaluator.hpp:54, from /<>/build/Python/ConsensusCore_wrap.cxx:6764: /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:230:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool Insert(const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:237:76: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] bool InsertAs(const std::string& name, const QuiverConfig& config) throw(InvalidInputError); ^~~~~ /<>/include/ConsensusCore/Quiver/QuiverConfig.hpp:241:63: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] const QuiverConfig& At(const std::string& name) const throw(InvalidInputError); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/SimpleRecursor.hpp:43, from /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:46, from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/build/Python/ConsensusCore_wrap.cxx:7581: /<>/include/ConsensusCore/Quiver/detail/RecursorBase.hpp:79:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp:43, from /<>/build/Python/ConsensusCore_wrap.cxx:7581: /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:63:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/MutationScorer.hpp:71:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ In file included from /<>/build/Python/ConsensusCore_wrap.cxx:7586: /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:58:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:62:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:66:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ /<>/include/ConsensusCore/Quiver/ReadScorer.hpp:70:13: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] throw(AlphaBetaMismatchException); ^~~~~ make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' running install running install_lib running build_py copying build/Python/ConsensusCore.py -> /<>/.pybuild/cpython3_3.7_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /<>/.pybuild/cpython3_3.7_pbconsensuscore/build creating /<>/debian/python3-pbconsensuscore/usr creating /<>/debian/python3-pbconsensuscore/usr/lib creating /<>/debian/python3-pbconsensuscore/usr/lib/python3.7 creating /<>/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages copying /<>/.pybuild/cpython3_3.7_pbconsensuscore/build/ConsensusCore.py -> /<>/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages copying /<>/.pybuild/cpython3_3.7_pbconsensuscore/build/_ConsensusCore.so -> /<>/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages byte-compiling /<>/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages/ConsensusCore.py to ConsensusCore.cpython-37.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/python3.7/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts dh_install -a -O--buildsystem=pybuild dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_python2 make[1]: Entering directory '/<>' dh_python2 I: dh_python2 fs:329: renaming _ConsensusCore.so to _ConsensusCore.i386-linux-gnu.so dh_numpy make[1]: Leaving directory '/<>' debian/rules override_dh_python3 make[1]: Entering directory '/<>' dh_python3 I: dh_python3 fs:329: renaming _ConsensusCore.so to _ConsensusCore.cpython-37m-i386-linux-gnu.so dh_numpy3 make[1]: Leaving directory '/<>' dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-pbconsensuscore/usr/lib/python3/dist-packages/_ConsensusCore.cpython-37m-i386-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages/_ConsensusCore.i386-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package libconsensuscore-dev: unknown substitution variable ${shlibs:Depends} dpkg-gencontrol: warning: package libconsensuscore-dev: unused substitution variable ${python3:Depends} dpkg-gencontrol: warning: package libconsensuscore-dev: 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 python-pbconsensuscore: unused substitution variable ${python3:Depends} 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 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 python-pbconsensuscore: unused substitution variable ${python3:Depends} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python:Versions} dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing libconsensuscore-dev (in debian/libconsensuscore-dev); do_strip: , oemstrip: pkgstriptranslations: processing python3-pbconsensuscore-dbgsym (in debian/.debhelper/python3-pbconsensuscore/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python-pbconsensuscore-dbgsym (in debian/.debhelper/python-pbconsensuscore/dbgsym-root); do_strip: , oemstrip: 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/python3-pbconsensuscore/dbgsym-root/DEBIAN/control, package python3-pbconsensuscore-dbgsym, directory debian/.debhelper/python3-pbconsensuscore/dbgsym-root dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pbconsensuscore/python3-pbconsensuscore-dbgsym_1.0.2-3build1_i386.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package libconsensuscore-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.0.2-3build1_i386.deb'. INFO: pkgstriptranslations version 143 pkgstriptranslations: processing python-pbconsensuscore (in debian/python-pbconsensuscore); do_strip: , oemstrip: 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_1.0.2-3build1_i386.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/python-pbconsensuscore/dbgsym-root/DEBIAN/control, package python-pbconsensuscore-dbgsym, directory debian/.debhelper/python-pbconsensuscore/dbgsym-root dpkg-deb: building package 'python-pbconsensuscore-dbgsym' in 'debian/.debhelper/scratch-space/build-python-pbconsensuscore/python-pbconsensuscore-dbgsym_1.0.2-3build1_i386.deb'. Renaming python3-pbconsensuscore-dbgsym_1.0.2-3build1_i386.deb to python3-pbconsensuscore-dbgsym_1.0.2-3build1_i386.ddeb Renaming python-pbconsensuscore-dbgsym_1.0.2-3build1_i386.deb to python-pbconsensuscore-dbgsym_1.0.2-3build1_i386.ddeb INFO: pkgstriptranslations version 143 pkgstriptranslations: processing python3-pbconsensuscore (in debian/python3-pbconsensuscore); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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_1.0.2-3build1_i386.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../consensuscore_1.0.2-3build1_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build consensuscore-1.0.2 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181103-1340 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ consensuscore_1.0.2-3build1_i386.changes: ----------------------------------------- Format: 1.8 Date: Sat, 03 Nov 2018 12:06:28 +0000 Source: consensuscore Binary: libconsensuscore-dev python-pbconsensuscore python3-pbconsensuscore Architecture: i386 Version: 1.0.2-3build1 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose 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 (1.0.2-3build1) disco; urgency=medium . * No-change rebuild to build without python3.6 support. Checksums-Sha1: feb9e88f27284da18ef112877e47d6cefe5e1cf6 7871 consensuscore_1.0.2-3build1_i386.buildinfo 463c22602c1f2cc5250000b43dba2774a5c90c12 484040 libconsensuscore-dev_1.0.2-3build1_i386.deb d7312bc929b2d3ff084db1d68c9092916cd40f6a 9114768 python-pbconsensuscore-dbgsym_1.0.2-3build1_i386.ddeb cb94bc723a7a64b1a377e73f123e07d18bf78647 658188 python-pbconsensuscore_1.0.2-3build1_i386.deb c77d5a876a84363a5550603f0b6cecf5ca3f7412 9153616 python3-pbconsensuscore-dbgsym_1.0.2-3build1_i386.ddeb 1382cd8469bc29e7f6a3b41f3fec2d2e5e3d6a76 660020 python3-pbconsensuscore_1.0.2-3build1_i386.deb Checksums-Sha256: 4eeff780f434b577b37c3cec97d2b61fc78bfc7925da5f3a4e8aafb1d32c3f61 7871 consensuscore_1.0.2-3build1_i386.buildinfo b49a869fa7491a364a611b5777d4f4acf102a35012cf63d5471198fb3d4874f5 484040 libconsensuscore-dev_1.0.2-3build1_i386.deb 39dd4731ff9d6ac6edb77a8687a5a512503dc2ac93ea9bfaf11b68b43859ee3b 9114768 python-pbconsensuscore-dbgsym_1.0.2-3build1_i386.ddeb a4407dec58949b74d5f557683a72bf5015aaf79368ca457046474b3b2a68c28a 658188 python-pbconsensuscore_1.0.2-3build1_i386.deb c980a56dc78360d236d13eea5c143497f5407cf611231a3c272459b65c2e2a52 9153616 python3-pbconsensuscore-dbgsym_1.0.2-3build1_i386.ddeb 403863e17f239089f3db5d454f98d475bcd6025c82226d44ffcc8216396bf248 660020 python3-pbconsensuscore_1.0.2-3build1_i386.deb Files: cc99636ead34adc39ce648afd7cb5042 7871 science optional consensuscore_1.0.2-3build1_i386.buildinfo 0b91a82d613d8ac0d3b0e2b40fab09ea 484040 libdevel optional libconsensuscore-dev_1.0.2-3build1_i386.deb 84634f1c9b469d6589ca8d1d31d9bd50 9114768 debug optional python-pbconsensuscore-dbgsym_1.0.2-3build1_i386.ddeb 878f98077919db62f2cf1d1035c5d7ee 658188 python optional python-pbconsensuscore_1.0.2-3build1_i386.deb bb0cc87cb31a40cdd182ae2b0b848365 9153616 debug optional python3-pbconsensuscore-dbgsym_1.0.2-3build1_i386.ddeb ce51158f6069a4030d42e3cef50a8abb 660020 python optional python3-pbconsensuscore_1.0.2-3build1_i386.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libconsensuscore-dev_1.0.2-3build1_i386.deb ------------------------------------------- new debian package, version 2.0. size 484040 bytes: control archive=2200 bytes. 813 bytes, 18 lines control 4237 bytes, 52 lines md5sums Package: libconsensuscore-dev Source: consensuscore Version: 1.0.2-3build1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3259 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 2018-11-03 12:06 ./ drwxr-xr-x root/root 0 2018-11-03 12:06 ./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 ./usr/include/ConsensusCore/Matrix/DenseMatrix.hpp -rw-r--r-- root/root 4994 2016-05-06 17:25 ./usr/include/ConsensusCore/Matrix/SparseMatrix-inl.hpp -rw-r--r-- root/root 3831 2016-05-06 17:25 ./usr/include/ConsensusCore/Matrix/SparseMatrix.hpp -rw-r--r-- root/root 8693 2016-05-06 17:25 ./usr/include/ConsensusCore/Matrix/SparseVector-inl.hpp -rw-r--r-- root/root 3508 2016-05-06 17:25 ./usr/include/ConsensusCore/Matrix/SparseVector.hpp -rw-r--r-- root/root 2010 2016-05-06 17:25 ./usr/include/ConsensusCore/Matrix/VectorL.hpp -rw-r--r-- root/root 4971 2016-05-06 17:25 ./usr/include/ConsensusCore/Mutation-inl.hpp -rw-r--r-- root/root 4443 2016-05-06 17:25 ./usr/include/ConsensusCore/Mutation.hpp drwxr-xr-x root/root 0 2016-05-06 17:25 ./usr/include/ConsensusCore/Poa/ -rw-r--r-- root/root 3856 2016-05-06 17:25 ./usr/include/ConsensusCore/Poa/PoaConsensus.hpp -rw-r--r-- root/root 4049 2016-05-06 17:25 ./usr/include/ConsensusCore/Poa/PoaGraph.hpp -rw-r--r-- root/root 1715 2016-05-06 17:25 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./usr/share/doc/libconsensuscore-dev/copyright python-pbconsensuscore_1.0.2-3build1_i386.deb --------------------------------------------- new debian package, version 2.0. size 658188 bytes: control archive=1292 bytes. 980 bytes, 19 lines control 683 bytes, 7 lines md5sums 172 bytes, 9 lines * postinst #!/bin/sh 283 bytes, 14 lines * prerm #!/bin/sh Package: python-pbconsensuscore Source: consensuscore Version: 1.0.2-3build1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2830 Depends: libc6 (>= 2.27), libgcc1 (>= 1:4.0), libstdc++6 (>= 5.2), python (<< 2.8), python (>= 2.7~), python-numpy (>= 1:1.14.3), python-numpy-abi9, python:any (<< 2.8), python:any (>= 2.7~) 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. 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