https://launchpad.net/ubuntu/+source/consensuscore/1.1.1+dfsg-1/+build/15626189 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-013 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... 9 Nov 08:13:48 ntpdate[1794]: adjust time server 10.211.37.1 offset 0.037274 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15626189 /home/buildd/filecache-default/727e394105280e93a16c79dcca0079cc298d61c4 Creating target for build PACKAGEBUILD-15626189 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15626189 Starting target for build PACKAGEBUILD-15626189 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15626189 '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-15626189 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=i386 PACKAGEBUILD-15626189 Updating target for build PACKAGEBUILD-15626189 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 [1005 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe i386 Packages [8721 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5052 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main i386 Packages [121 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [72.9 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe i386 Packages [170 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [117 kB] Fetched 16.2 MB in 5s (2965 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 dash dmsetup findutils g++ g++-8 gcc gcc-8 gcc-8-base hostname init init-system-helpers libapparmor1 libasan5 libatomic1 libaudit-common libaudit1 libbinutils libcap-ng0 libcc1-0 libdb5.3 libdevmapper1.02.1 libgcc-8-dev libgcc1 libgdbm-compat4 libgomp1 libgpg-error0 libitm1 libkmod2 libmpx2 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libstdc++-8-dev libstdc++6 libsystemd0 libubsan1 libudev1 linux-libc-dev lockfile-progs perl perl-base systemd systemd-sysv tzdata 52 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 46.9 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 dash i386 0.5.10.2-1 [94.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-proposed/main i386 findutils i386 4.6.0+git+20181018-1 [307 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed/main i386 hostname i386 3.21 [11.6 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main i386 perl-modules-5.28 all 5.28.0-3 [2818 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main i386 libgdbm6 i386 1.18.1-1 [32.1 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main i386 libgdbm-compat4 i386 1.18.1-1 [6704 B] Get:8 http://ftpmaster.internal/ubuntu disco/main i386 libperl5.28 i386 5.28.0-3 [3436 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main i386 perl i386 5.28.0-3 [204 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main i386 perl-base i386 5.28.0-3 [1600 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libdb5.3 i386 5.3.28+dfsg1-0.2 [737 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main i386 init-system-helpers all 1.55 [38.5 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main i386 systemd-sysv i386 239-7ubuntu10.1 [9400 B] Get:14 http://ftpmaster.internal/ubuntu disco/main i386 libapparmor1 i386 2.12-4ubuntu10 [31.3 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main i386 libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:16 http://ftpmaster.internal/ubuntu disco/main i386 libcap-ng0 i386 0.7.9-1build1 [11.1 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main i386 libaudit1 i386 1:2.8.3-1ubuntu3 [40.0 kB] Get:18 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libgpg-error0 i386 1.32-3 [60.5 kB] Get:19 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libkmod2 i386 25-1ubuntu1.1 [47.7 kB] Get:20 http://ftpmaster.internal/ubuntu disco-proposed/main i386 systemd i386 239-7ubuntu10.1 [3067 kB] Get:21 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libsystemd0 i386 239-7ubuntu10.1 [228 kB] Get:22 http://ftpmaster.internal/ubuntu disco-proposed/main i386 init i386 1.55 [6476 B] Get:23 http://ftpmaster.internal/ubuntu disco/main i386 libquadmath0 i386 8.2.0-9ubuntu1 [208 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main i386 libubsan1 i386 8.2.0-9ubuntu1 [138 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main i386 libitm1 i386 8.2.0-9ubuntu1 [30.8 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main i386 libasan5 i386 8.2.0-9ubuntu1 [375 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main i386 gcc-8-base i386 8.2.0-9ubuntu1 [18.6 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main i386 libstdc++6 i386 8.2.0-9ubuntu1 [430 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main i386 libgomp1 i386 8.2.0-9ubuntu1 [80.7 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main i386 libatomic1 i386 8.2.0-9ubuntu1 [9604 B] Get:31 http://ftpmaster.internal/ubuntu disco/main i386 libmpx2 i386 8.2.0-9ubuntu1 [13.0 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main i386 cpp-8 i386 8.2.0-9ubuntu1 [7537 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main i386 libcc1-0 i386 8.2.0-9ubuntu1 [41.9 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main i386 gcc-8 i386 8.2.0-9ubuntu1 [8330 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main i386 g++-8 i386 8.2.0-9ubuntu1 [8444 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main i386 libstdc++-8-dev i386 8.2.0-9ubuntu1 [1586 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main i386 libgcc-8-dev i386 8.2.0-9ubuntu1 [2299 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main i386 libgcc1 i386 1:8.2.0-9ubuntu1 [48.1 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main i386 libbinutils i386 2.31.1-7ubuntu1 [518 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main i386 binutils-common i386 2.31.1-7ubuntu1 [194 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main i386 binutils i386 2.31.1-7ubuntu1 [3392 B] Get:42 http://ftpmaster.internal/ubuntu disco/main i386 binutils-i686-linux-gnu i386 2.31.1-7ubuntu1 [1985 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main i386 libselinux1 i386 2.8-1build2 [73.5 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main i386 libsemanage-common all 2.8-1build2 [6892 B] Get:45 http://ftpmaster.internal/ubuntu disco/main i386 libsemanage1 i386 2.8-1build2 [93.8 kB] Get:46 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libudev1 i386 239-7ubuntu10.1 [57.6 kB] Get:47 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libseccomp2 i386 2.3.3-3ubuntu2 [35.6 kB] Get:48 http://ftpmaster.internal/ubuntu disco-proposed/main i386 libdevmapper1.02.1 i386 2:1.02.145-4.1ubuntu4 [125 kB] Get:49 http://ftpmaster.internal/ubuntu disco-proposed/main i386 dmsetup i386 2:1.02.145-4.1ubuntu4 [70.4 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main i386 tzdata all 2018g-1 [188 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main i386 g++ i386 4:8.2.0-2ubuntu2 [1616 B] Get:52 http://ftpmaster.internal/ubuntu disco/main i386 gcc i386 4:8.2.0-2ubuntu2 [5272 B] Get:53 http://ftpmaster.internal/ubuntu disco/main i386 cpp i386 4:8.2.0-2ubuntu2 [27.6 kB] Get:54 http://ftpmaster.internal/ubuntu disco-proposed/main i386 linux-libc-dev i386 4.18.0-11.12 [1040 kB] Get:55 http://ftpmaster.internal/ubuntu disco-proposed/main i386 lockfile-progs i386 0.1.18 [9856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 46.9 MB in 2s (27.2 MB/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 .../dash_0.5.10.2-1_i386.deb ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Unpacking dash (0.5.10.2-1) over (0.5.8-2.10) ... Setting up dash (0.5.10.2-1) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by bash' Adding 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (Reading database ... 12644 files and directories currently installed.) Preparing to unpack .../findutils_4.6.0+git+20181018-1_i386.deb ... Unpacking findutils (4.6.0+git+20181018-1) over (4.6.0+git+20180808-2) ... Setting up findutils (4.6.0+git+20181018-1) ... (Reading database ... 12644 files and directories currently installed.) Preparing to unpack .../hostname_3.21_i386.deb ... Unpacking hostname (3.21) over (3.20) ... Setting up hostname (3.21) ... (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) ... 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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: Fri Nov 9 08:14:18 UTC 2018. Universal Time is now: Fri Nov 9 08:14:18 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up init (1.55) ... 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 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 dmsetup (2:1.02.145-4.1ubuntu4) ... Setting up libgdbm-compat4:i386 (1.18.1-1) ... Setting up lockfile-progs (0.1.18) ... 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-15626189 i386 disco-proposed -c chroot:build-PACKAGEBUILD-15626189 --arch=i386 --dist=disco-proposed --nolog consensuscore_1.1.1+dfsg-1.dsc Initiating build PACKAGEBUILD-15626189 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 lcy01-amd64-013.buildd +==============================================================================+ | consensuscore 1.1.1+dfsg-1 (i386) 09 Nov 2018 08:14 | +==============================================================================+ Package: consensuscore Version: 1.1.1+dfsg-1 Source Version: 1.1.1+dfsg-1 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/consensuscore-YwGTEt/consensuscore-1.1.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/consensuscore-YwGTEt' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15626189/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- consensuscore_1.1.1+dfsg-1.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-w7bNDx/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-w7bNDx/apt_archive ./ InRelease Get:2 copy:/<>/resolver-w7bNDx/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-w7bNDx/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-w7bNDx/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-w7bNDx/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (195 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-w7bNDx/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-MR8uwE/apt_archive/sbuild-build-depends-consensuscore-dummy.deb'. Ign:1 copy:/<>/resolver-MR8uwE/apt_archive ./ InRelease Get:2 copy:/<>/resolver-MR8uwE/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-MR8uwE/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-MR8uwE/apt_archive ./ Sources [274 B] Get:5 copy:/<>/resolver-MR8uwE/apt_archive ./ Packages [594 B] Fetched 2987 B in 0s (191 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: libgdbm5 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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http://ftpmaster.internal/ubuntu disco/main i386 python3-pkg-resources all 40.5.0-1 [99.6 kB] Get:85 http://ftpmaster.internal/ubuntu disco/main i386 python3-setuptools all 40.5.0-1 [249 kB] Get:86 http://ftpmaster.internal/ubuntu disco/universe i386 swig3.0 i386 3.0.12-1.2 [1158 kB] Get:87 http://ftpmaster.internal/ubuntu disco/universe i386 swig i386 3.0.12-1.2 [6464 B] Get:88 http://ftpmaster.internal/ubuntu disco/main i386 dh-exec i386 0.23build1 [24.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 125 MB in 6s (21.2 MB/s) Selecting previously unselected package libpython3.7-minimal:i386. 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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 (1:1.16.1-4) ... 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 (2.8.4-3) ... 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 (40.5.0-1) ... 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 (3.7.1-1ubuntu3) ... Setting up python3-distutils (3.7.1-1ubuntu3) ... 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 (40.5.0-1) ... Setting up python-numpy (1:1.14.5-1ubuntu7) ... Setting up python3-setuptools (40.5.0-1) ... Setting up dh-python (3.20180927ubuntu2) ... Setting up python-all (2.7.15-3) ... Setting up python-setuptools (40.5.0-1) ... 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_1:1.16.1-4 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_0.5.10.2-1 debconf_1.5.69 debhelper_11.3.2ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-exec_0.23build1 dh-python_3.20180927ubuntu2 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+20181018-1 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_3.21 init_1.55 init-system-helpers_1.55 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_1.64-1 libargon2-1_0~20171227-0.1 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libubsan1_8.2.0-9ubuntu1 libudev1_239-7ubuntu10.1 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_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1ubuntu1 make_4.2.1-1.2 man-db_2.8.4-3 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_40.5.0-1 python-setuptools_40.5.0-1 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_3.7.1-1ubuntu3 python3-lib2to3_3.7.1-1ubuntu3 python3-minimal_3.7.1-1ubuntu1 python3-numpy_1:1.14.5-1ubuntu7 python3-pkg-resources_40.5.0-1 python3-setuptools_40.5.0-1 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_239-7ubuntu10.1 systemd-sysv_239-7ubuntu10.1 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 Tue Oct 9 16:10:34 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./consensuscore_1.1.1+dfsg-1.dsc dpkg-source: info: extracting consensuscore in consensuscore-1.1.1+dfsg dpkg-source: info: unpacking consensuscore_1.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking consensuscore_1.1.1+dfsg-1.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-15626189 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15626189 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15626189 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 1.1.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build consensuscore-1.1.1+dfsg 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 '/<>/consensuscore-1.1.1+dfsg/.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 '/<>/consensuscore-1.1.1+dfsg/.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_STD = c++14 make[1]: Entering directory '/<>/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/<>/consensuscore-1.1.1+dfsg' mkdir -p /<>/consensuscore-1.1.1+dfsg/build/C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Coverage.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Utils.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Statistics/Binomial.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Binomial.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Features.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Features.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Logging.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Logging.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Utils.o -MM src/C++/Utils.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Utils.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Align/PairwiseAlignment.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Version.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Version.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Coverage.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Sequence.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Sequence.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Mutation.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Read.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Read.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Features.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Feature.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraph.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Feature.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Checksum.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Version.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Binomial.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SseRecursor.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SimpleRecursor.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/Diploid.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConsensus.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/Diploid.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/detail/RecursorBase.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.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:190:16: required from here src/C++/Quiver/MutationScorer.cpp:30:7: 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:191:16: required from here src/C++/Quiver/MutationScorer.cpp:30:7: 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:192:16: required from here src/C++/Quiver/MutationScorer.cpp:30:7: 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:193:16: required from here src/C++/Quiver/MutationScorer.cpp:30:7: 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:194:16: required from here src/C++/Quiver/MutationScorer.cpp:30:7: 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:195:16: required from here src/C++/Quiver/MutationScorer.cpp:30:7: 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:196:16: required from here src/C++/Quiver/MutationScorer.cpp:30:7: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -pedantic -std=c++14 -Wall -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c src/C++/Edna/EdnaCounts.cpp -o /<>/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -MT /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d ar crs /<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /<>/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /<>/consensuscore-1.1.1+dfsg/build/C++/Utils.o /<>/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /<>/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /<>/consensuscore-1.1.1+dfsg/build/C++/Features.o /<>/consensuscore-1.1.1+dfsg/build/C++/Logging.o /<>/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o /<>/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /<>/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o /<>/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /<>/consensuscore-1.1.1+dfsg/build/C++/Version.o /<>/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /<>/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /<>/consensuscore-1.1.1+dfsg/build/C++/Read.o /<>/consensuscore-1.1.1+dfsg/build/C++/Feature.o /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o /<>/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /<>/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /<>/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /<>/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /<>/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /<>/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /<>/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /<>/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /<>/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /<>/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /<>/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /<>/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /<>/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /<>/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /<>/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /<>/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o touch /<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a make[2]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/<>/consensuscore-1.1.1+dfsg' mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /<>/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I /usr/include/python2.7 -I /usr/lib/python2.7/dist-packages/numpy/core/include /<>/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /<>/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' 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_STD = c++14 make[1]: Entering directory '/<>/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/<>/consensuscore-1.1.1+dfsg' make[2]: '/<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/<>/consensuscore-1.1.1+dfsg' mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /<>/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.7m -I /usr/lib/python3/dist-packages/numpy/core/include /<>/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /<>/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/consensuscore-1.1.1+dfsg' /usr/bin/make test make[2]: Entering directory '/<>/consensuscore-1.1.1+dfsg' /usr/bin/make -f make/Cpp.mk -j8 make[3]: Entering directory '/<>/consensuscore-1.1.1+dfsg' make[3]: '/<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[3]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make[3]: Entering directory '/<>/consensuscore-1.1.1+dfsg' mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestSparseVector.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestPoaConsensus.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestMutationScorer.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/ParameterSettings.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestRecursors.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestCoverage.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestPairwiseAlignment.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestMutations.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestMultiReadMutationScorer.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestMutationEnumerator.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestDiploidQuiver.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /<>/consensuscore-1.1.1+dfsg/src/Tests/TestMatrixFacades.cpp -o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now /<>/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /<>/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /<>/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -I/<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 /<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock-gtest-all.cc /<>/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock_main.cc -lpthread -o /<>/consensuscore-1.1.1+dfsg/build/Tests/test-runner GTEST_OUTPUT="xml:tests-summary.xml" /<>/consensuscore-1.1.1+dfsg/build/Tests/test-runner Running main() from gmock_main.cc [==========] Running 158 tests from 29 test cases. [----------] Global test environment set-up. [----------] 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 (0 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (1 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (0 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (0 ms) [----------] 4 tests from PoaGraph (2 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (0 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (0 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) [ RUN ] PoaConsensus.SmallTilingTest [ OK ] PoaConsensus.SmallTilingTest (0 ms) [ RUN ] PoaConsensus.TestVerboseGraphVizOutput [ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png sh: 1: dot: not found [ OK ] PoaConsensus.TestLocalStaggered (6 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (1 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (1033 ms) [----------] 8 tests from PoaConsensus (1041 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (64 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (70 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (81 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (55 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (8 ms) [----------] 5 tests from QvEvaluatorTest (279 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 (2 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/0 (4 ms total) [----------] 8 tests from MutationScorerTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/1.BasicTest [ OK ] MutationScorerTest/1.BasicTest (0 ms) [ RUN ] MutationScorerTest/1.CopyTest [ OK ] MutationScorerTest/1.CopyTest (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtBeginning [ OK ] MutationScorerTest/1.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtEnd [ OK ] MutationScorerTest/1.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/1.TinyTemplate [ OK ] MutationScorerTest/1.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/1.TemplateMutationWorkflow [ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideInsertionTest [ OK ] MutationScorerTest/1.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/1 (4 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest [ OK ] MutationScorerTest/2.BasicTest (0 ms) [ RUN ] MutationScorerTest/2.CopyTest [ OK ] MutationScorerTest/2.CopyTest (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtBeginning [ OK ] MutationScorerTest/2.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtEnd [ OK ] MutationScorerTest/2.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/2.TinyTemplate [ OK ] MutationScorerTest/2.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/2.TemplateMutationWorkflow [ OK ] MutationScorerTest/2.TemplateMutationWorkflow (1 ms) [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/2 (4 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest [ OK ] MutationScorerTest/3.BasicTest (0 ms) [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning [ OK ] MutationScorerTest/3.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest [ OK ] MutationScorerTest/3.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest [ OK ] MutationScorerTest/3.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/3 (5 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 (1 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 (1 ms) [----------] 7 tests from RecursorTest/0 (2 ms total) [----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/1.SmallMatchTest [ OK ] RecursorTest/1.SmallMatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMismatchTest [ OK ] RecursorTest/1.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMergeTest [ OK ] RecursorTest/1.SmallMergeTest (0 ms) [ RUN ] RecursorTest/1.MediumSizedTest [ OK ] RecursorTest/1.MediumSizedTest (4 ms) [ RUN ] RecursorTest/1.LinkTest [ OK ] RecursorTest/1.LinkTest (0 ms) [ RUN ] RecursorTest/1.ExtendAlphaTest [ OK ] RecursorTest/1.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/1.ExtendBetaTest [ OK ] RecursorTest/1.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/1 (4 ms total) [----------] 7 tests from RecursorTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/2.SmallMatchTest [ OK ] RecursorTest/2.SmallMatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMismatchTest [ OK ] RecursorTest/2.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/2.SmallMergeTest [ OK ] RecursorTest/2.SmallMergeTest (0 ms) [ RUN ] RecursorTest/2.MediumSizedTest [ OK ] RecursorTest/2.MediumSizedTest (4 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (0 ms) [ RUN ] RecursorTest/2.ExtendAlphaTest [ OK ] RecursorTest/2.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/2.ExtendBetaTest [ OK ] RecursorTest/2.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/2 (5 ms total) [----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/3.SmallMatchTest [ OK ] RecursorTest/3.SmallMatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMismatchTest [ OK ] RecursorTest/3.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest [ OK ] RecursorTest/3.MediumSizedTest (3 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/3 (5 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (30 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (31 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (33 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (39 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (38 ms) [----------] 5 tests from RecursorFuzzTest/0 (171 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (81 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (82 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (83 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (40 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (39 ms) [----------] 5 tests from RecursorFuzzTest/1 (327 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (101 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (103 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (112 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (29 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (29 ms) [----------] 5 tests from RecursorFuzzTest/2 (375 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (83 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (84 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (86 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (27 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (28 ms) [----------] 5 tests from RecursorFuzzTest/3 (310 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (1 ms) [ RUN ] CoverageTests.CoveredIntervalsTest2 [ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) [----------] 3 tests from CoverageTests (1 ms total) [----------] 3 tests from PairwiseAlignmentTests [ RUN ] PairwiseAlignmentTests.RepresentationTests [ OK ] PairwiseAlignmentTests.RepresentationTests (0 ms) [ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests [ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms) [ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest [ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (0 ms) [----------] 3 tests from PairwiseAlignmentTests (1 ms total) [----------] 2 tests from AffineAlignmentTests [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest [ OK ] AffineAlignmentTests.LargeGapTest (32 ms) [----------] 2 tests from AffineAlignmentTests (32 ms total) [----------] 1 test from IupacAlignmentTests [ RUN ] IupacAlignmentTests.BasicTest [ OK ] IupacAlignmentTests.BasicTest (0 ms) [----------] 1 test from IupacAlignmentTests (0 ms total) [----------] 1 test from LinearAlignmentTests [ RUN ] LinearAlignmentTests.BasicTest [ OK ] LinearAlignmentTests.BasicTest (1 ms) [----------] 1 test from LinearAlignmentTests (1 ms total) [----------] 7 tests from MutationTest [ RUN ] MutationTest.BasicTest [ OK ] MutationTest.BasicTest (0 ms) [ RUN ] MutationTest.DeleteTest [ OK ] MutationTest.DeleteTest (0 ms) [ RUN ] MutationTest.InsertTest [ OK ] MutationTest.InsertTest (0 ms) [ RUN ] MutationTest.ApplyMutationsTest [ OK ] MutationTest.ApplyMutationsTest (0 ms) [ RUN ] MutationTest.ApplyMutationsToSamePositionTest [ OK ] MutationTest.ApplyMutationsToSamePositionTest (0 ms) [ RUN ] MutationTest.MutationsToTranscript [ OK ] MutationTest.MutationsToTranscript (0 ms) [ RUN ] MutationTest.MutatedTemplatePositionsTest [ OK ] MutationTest.MutatedTemplatePositionsTest (0 ms) [----------] 7 tests from MutationTest (1 ms total) [----------] 1 test from QuiverConfigTableTests [ RUN ] QuiverConfigTableTests.IllegalChemistry [ OK ] QuiverConfigTableTests.IllegalChemistry (0 ms) [----------] 1 test from QuiverConfigTableTests (0 ms total) [----------] 3 tests from MutationOrientationTests [ RUN ] MutationOrientationTests.ReadScoresMutation1 [ OK ] MutationOrientationTests.ReadScoresMutation1 (0 ms) [ RUN ] MutationOrientationTests.ReadScoresMutation2 [ OK ] MutationOrientationTests.ReadScoresMutation2 (0 ms) [ RUN ] MutationOrientationTests.OrientedMutation [ OK ] MutationOrientationTests.OrientedMutation (0 ms) [----------] 3 tests from MutationOrientationTests (0 ms total) [----------] 11 tests from MultiReadMutationScorerTest/0, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MultiReadMutationScorerTest/0.Template [ OK ] MultiReadMutationScorerTest/0.Template (0 ms) [ RUN ] MultiReadMutationScorerTest/0.BasicTest [ OK ] MultiReadMutationScorerTest/0.BasicTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest [ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest [ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 [ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest [ OK ] MultiReadMutationScorerTest/0.CopyTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (1 ms) [----------] 11 tests from MultiReadMutationScorerTest/0 (8 ms total) [----------] 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 (3 ms) [ RUN ] MutationEnumerationTest.TestDinucleotideMutations [ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) [----------] 4 tests from MutationEnumerationTest (3 ms total) [----------] 11 tests from MatrixTest/0, where TypeParam = ConsensusCore::DenseMatrix [ RUN ] MatrixTest/0.Basic [ OK ] MatrixTest/0.Basic (0 ms) [ RUN ] MatrixTest/0.Nullability [ OK ] MatrixTest/0.Nullability (0 ms) [ RUN ] MatrixTest/0.Ranges [ OK ] MatrixTest/0.Ranges (0 ms) [ RUN ] MatrixTest/0.IsColumnEmpty [ OK ] MatrixTest/0.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/0.SSE [ OK ] MatrixTest/0.SSE (0 ms) [ RUN ] MatrixTest/0.ToHostArray [ OK ] MatrixTest/0.ToHostArray (0 ms) [ RUN ] MatrixTest/0.NonSequentialAccess [ OK ] MatrixTest/0.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/0.Holes [ OK ] MatrixTest/0.Holes (0 ms) [ RUN ] MatrixTest/0.BigBandedMatrix N13ConsensusCore11DenseMatrixE : 1000000 [ OK ] MatrixTest/0.BigBandedMatrix (11 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 (12 ms total) [----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix [ RUN ] MatrixTest/1.Basic [ OK ] MatrixTest/1.Basic (1 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 (10 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 (12 ms total) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (2614 ms total) [ PASSED ] 158 tests. make[3]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make[2]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' 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 /<>/consensuscore-1.1.1+dfsg/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_STD = c++14 make[1]: Entering directory '/<>/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/<>/consensuscore-1.1.1+dfsg' make[2]: '/<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/<>/consensuscore-1.1.1+dfsg' mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /<>/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I /usr/include/python2.7 -I /usr/lib/python2.7/dist-packages/numpy/core/include /<>/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /<>/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' running install running install_lib running build_py copying build/Python/ConsensusCore.py -> /<>/consensuscore-1.1.1+dfsg/.pybuild/cpython2_2.7_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /<>/consensuscore-1.1.1+dfsg/.pybuild/cpython2_2.7_pbconsensuscore/build creating /<>/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr creating /<>/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib creating /<>/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib/python2.7 creating /<>/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages copying /<>/consensuscore-1.1.1+dfsg/.pybuild/cpython2_2.7_pbconsensuscore/build/_ConsensusCore.so -> /<>/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages copying /<>/consensuscore-1.1.1+dfsg/.pybuild/cpython2_2.7_pbconsensuscore/build/ConsensusCore.py -> /<>/consensuscore-1.1.1+dfsg/debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages byte-compiling /<>/consensuscore-1.1.1+dfsg/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 /<>/consensuscore-1.1.1+dfsg/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 /<>/consensuscore-1.1.1+dfsg/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_STD = c++14 make[1]: Entering directory '/<>/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/<>/consensuscore-1.1.1+dfsg' make[2]: '/<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/<>/consensuscore-1.1.1+dfsg' mkdir -p /<>/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig3.0 /usr/bin/swig -Wall -c++ -python -builtin -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /<>/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /<>/consensuscore-1.1.1+dfsg/include/ConsensusCore/Poa/PoaConsensus.hpp:24: Warning 309: private inheritance from base 'noncopyable' (ignored). g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/<>/consensuscore-1.1.1+dfsg/include -I/<>/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.7m -I /usr/lib/python3/dist-packages/numpy/core/include /<>/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /<>/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /<>/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' running install running install_lib running build_py copying build/Python/ConsensusCore.py -> /<>/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.7_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /<>/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.7_pbconsensuscore/build creating /<>/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr creating /<>/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib creating /<>/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.7 creating /<>/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages copying /<>/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.7_pbconsensuscore/build/_ConsensusCore.so -> /<>/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages copying /<>/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.7_pbconsensuscore/build/ConsensusCore.py -> /<>/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.7/dist-packages byte-compiling /<>/consensuscore-1.1.1+dfsg/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 /<>/consensuscore-1.1.1+dfsg/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 '/<>/consensuscore-1.1.1+dfsg' dh_python2 I: dh_python2 fs:329: renaming _ConsensusCore.so to _ConsensusCore.i386-linux-gnu.so dh_numpy make[1]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' debian/rules override_dh_python3 make[1]: Entering directory '/<>/consensuscore-1.1.1+dfsg' dh_python3 I: dh_python3 fs:329: renaming _ConsensusCore.so to _ConsensusCore.cpython-37m-i386-linux-gnu.so dh_numpy3 make[1]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' 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/python-pbconsensuscore/usr/lib/python2.7/dist-packages/_ConsensusCore.i386-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-pbconsensuscore/usr/lib/python3/dist-packages/_ConsensusCore.cpython-37m-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 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} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python3:Versions} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python:Depends} dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing libconsensuscore-dev (in debian/libconsensuscore-dev); do_strip: , oemstrip: pkgstriptranslations: processing python-pbconsensuscore-dbgsym (in debian/.debhelper/python-pbconsensuscore/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python3-pbconsensuscore-dbgsym (in debian/.debhelper/python3-pbconsensuscore/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libconsensuscore-dev/DEBIAN/control, package libconsensuscore-dev, directory debian/libconsensuscore-dev pkgstripfiles: processing control file: debian/.debhelper/python-pbconsensuscore/dbgsym-root/DEBIAN/control, package python-pbconsensuscore-dbgsym, directory debian/.debhelper/python-pbconsensuscore/dbgsym-root dpkg-deb: building package 'python-pbconsensuscore-dbgsym' in 'debian/.debhelper/scratch-space/build-python-pbconsensuscore/python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package libconsensuscore-dev ... pkgstripfiles: No PNG files. 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_1.1.1+dfsg-1_i386.deb'. dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-1_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_1.1.1+dfsg-1_i386.deb'. Renaming python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.deb to python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.ddeb INFO: pkgstriptranslations version 143 Renaming python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.deb to python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.ddeb 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_1.1.1+dfsg-1_i386.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../consensuscore_1.1.1+dfsg-1_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build consensuscore-1.1.1+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181109-0826 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ consensuscore_1.1.1+dfsg-1_i386.changes: ---------------------------------------- Format: 1.8 Date: Tue, 09 Oct 2018 17:43:54 +0200 Source: consensuscore Binary: libconsensuscore-dev python-pbconsensuscore python3-pbconsensuscore Architecture: i386 Version: 1.1.1+dfsg-1 Distribution: disco-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille 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 (1.1.1+dfsg-1) unstable; urgency=medium . * Team upload * New upstream release * Exclude precompiled binaries * Standards-Version: 4.2.1 Checksums-Sha1: 9e859e6ef18412683384649f96bb2da65aa05e6b 7860 consensuscore_1.1.1+dfsg-1_i386.buildinfo 46fbd939a1e423b5f1bb1593d936c8c194af3072 467128 libconsensuscore-dev_1.1.1+dfsg-1_i386.deb bf39b86fae0dff231fe922d9fd476bba41d310b6 9327268 python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.ddeb 9e3d5ab198263e63e2ff737fd003d609147ce0f3 644064 python-pbconsensuscore_1.1.1+dfsg-1_i386.deb 3d48eeea281e2a4306e5d41982092ee50ff9bc4d 9371768 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.ddeb a99b84618b58815d42a95499d1b020d55f28e130 646168 python3-pbconsensuscore_1.1.1+dfsg-1_i386.deb Checksums-Sha256: 40ad95ced7c45e221796ae4bd3b66338c4d759d684b5f4e96675688e112c6fb9 7860 consensuscore_1.1.1+dfsg-1_i386.buildinfo 9eadccabd9a8e18291e94f48c5162f4a29060a18cb77506ec58d085e066bf5f0 467128 libconsensuscore-dev_1.1.1+dfsg-1_i386.deb 57d97951f8bcd3066916b17dcb6b955b6ea9247d11465b65a5543598689cefe6 9327268 python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.ddeb f953940c7e6af735906ee1af481ea74aaf7099f01cc1df5f79518eeae0c64e4c 644064 python-pbconsensuscore_1.1.1+dfsg-1_i386.deb 3303b309f39aa491a2a3596a7e6097ed6ca437231c9febc947715dd254a8be2b 9371768 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.ddeb ed825f97c8b7c6076ffda1edac1f5028c182a92ad53ade648d1b6beb5fe64e54 646168 python3-pbconsensuscore_1.1.1+dfsg-1_i386.deb Files: 6e59fcf7eee844d79893cdb19850a041 7860 science optional consensuscore_1.1.1+dfsg-1_i386.buildinfo 3f17de66174665d6fa7fb708195d120a 467128 libdevel optional libconsensuscore-dev_1.1.1+dfsg-1_i386.deb cc555de801e8180d27bb2c908b01c0b8 9327268 debug optional python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.ddeb 66832c087ed001f0a773b147d89eebec 644064 python optional python-pbconsensuscore_1.1.1+dfsg-1_i386.deb 27dd58a44f26cd7d6af5825271d7f6cb 9371768 debug optional python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_i386.ddeb 12a30f57a08e71dc0ba22711a4bc1d34 646168 python optional python3-pbconsensuscore_1.1.1+dfsg-1_i386.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libconsensuscore-dev_1.1.1+dfsg-1_i386.deb ------------------------------------------ new debian package, version 2.0. size 467128 bytes: control archive=2224 bytes. 812 bytes, 18 lines control 4295 bytes, 53 lines md5sums Package: libconsensuscore-dev Source: consensuscore Version: 1.1.1+dfsg-1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3084 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 2018-10-09 15:43 ./ drwxr-xr-x root/root 0 2018-10-09 15:43 ./usr/ drwxr-xr-x root/root 0 2018-08-14 14:23 ./usr/include/ drwxr-xr-x root/root 0 2018-08-14 14:23 ./usr/include/ConsensusCore/ drwxr-xr-x root/root 0 2018-08-14 14:23 ./usr/include/ConsensusCore/Align/ -rw-r--r-- root/root 1214 2018-08-14 14:23 ./usr/include/ConsensusCore/Align/AffineAlignment.hpp -rw-r--r-- root/root 775 2018-08-14 14:23 ./usr/include/ConsensusCore/Align/AlignConfig.hpp -rw-r--r-- root/root 565 2018-08-14 14:23 ./usr/include/ConsensusCore/Align/LinearAlignment.hpp -rw-r--r-- root/root 1956 2018-08-14 14:23 ./usr/include/ConsensusCore/Align/PairwiseAlignment.hpp -rw-r--r-- root/root 196 2018-08-14 14:23 ./usr/include/ConsensusCore/Checksum.hpp -rw-r--r-- root/root 653 2018-08-14 14:23 ./usr/include/ConsensusCore/Coverage.hpp drwxr-xr-x root/root 0 2018-08-14 14:23 ./usr/include/ConsensusCore/Edna/ -rw-r--r-- root/root 792 2018-08-14 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./usr/include/ConsensusCore/Poa/RangeFinder.hpp drwxr-xr-x root/root 0 2018-08-14 14:23 ./usr/include/ConsensusCore/Quiver/ -rw-r--r-- root/root 531 2018-08-14 14:23 ./usr/include/ConsensusCore/Quiver/Diploid.hpp -rw-r--r-- root/root 7338 2018-08-14 14:23 ./usr/include/ConsensusCore/Quiver/MultiReadMutationScorer.hpp -rw-r--r-- root/root 1178 2018-08-14 14:23 ./usr/include/ConsensusCore/Quiver/MutationEnumerator-inl.hpp -rw-r--r-- root/root 1776 2018-08-14 14:23 ./usr/include/ConsensusCore/Quiver/MutationEnumerator.hpp -rw-r--r-- root/root 1924 2018-08-14 14:23 ./usr/include/ConsensusCore/Quiver/MutationScorer.hpp -rw-r--r-- root/root 5260 2018-08-14 14:23 ./usr/include/ConsensusCore/Quiver/QuiverConfig.hpp -rw-r--r-- root/root 933 2018-08-14 14:23 ./usr/include/ConsensusCore/Quiver/QuiverConsensus.hpp -rw-r--r-- root/root 6705 2018-08-14 14:23 ./usr/include/ConsensusCore/Quiver/QvEvaluator.hpp -rw-r--r-- root/root 773 2018-08-14 14:23 ./usr/include/ConsensusCore/Quiver/ReadScorer.hpp 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./usr/share/doc/libconsensuscore-dev/copyright python-pbconsensuscore_1.1.1+dfsg-1_i386.deb -------------------------------------------- new debian package, version 2.0. size 644064 bytes: control archive=1296 bytes. 979 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: 1.1.1+dfsg-1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2790 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.4), 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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