https://launchpad.net/ubuntu/+source/consensuscore/1.1.1+dfsg-1/+build/15626188 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-012 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 08:13:58 ntpdate[1806]: adjust time server 10.211.37.1 offset -0.000338 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15626188 /home/buildd/filecache-default/b71572c9405b6ce6ff1d1ad001cf764bb07f52ae Creating target for build PACKAGEBUILD-15626188 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15626188 Starting target for build PACKAGEBUILD-15626188 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15626188 '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-15626188 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15626188 Updating target for build PACKAGEBUILD-15626188 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 amd64 Packages [1018 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe amd64 Packages [8777 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5052 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 Packages [129 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [72.9 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 Packages [179 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [117 kB] Fetched 16.3 MB in 7s (2368 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-x86-64-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 libitm1 libkmod2 liblsan0 libmpx2 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libstdc++-8-dev libstdc++6 libsystemd0 libtsan0 libubsan1 libudev1 linux-libc-dev lockfile-progs perl perl-base sed systemd systemd-sysv tzdata 54 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 46.1 MB of archives. After this operation, 48.7 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main amd64 base-files amd64 10.1ubuntu8 [60.1 kB] Get:2 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 dash amd64 0.5.10.2-1 [89.3 kB] Get:3 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 findutils amd64 4.6.0+git+20181018-1 [295 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 hostname amd64 3.21 [11.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 perl-modules-5.28 all 5.28.0-3 [2818 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main amd64 libgdbm6 amd64 1.18.1-1 [27.8 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main amd64 libgdbm-compat4 amd64 1.18.1-1 [6148 B] Get:8 http://ftpmaster.internal/ubuntu disco/main amd64 libperl5.28 amd64 5.28.0-3 [3804 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main amd64 perl amd64 5.28.0-3 [204 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main amd64 perl-base amd64 5.28.0-3 [1510 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.2 [672 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 sed amd64 4.5-2 [186 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 init-system-helpers all 1.55 [38.5 kB] Get:14 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 systemd-sysv amd64 239-7ubuntu10.1 [9404 B] Get:15 http://ftpmaster.internal/ubuntu disco/main amd64 libapparmor1 amd64 2.12-4ubuntu10 [29.9 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main amd64 libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:17 http://ftpmaster.internal/ubuntu disco/main amd64 libcap-ng0 amd64 0.7.9-1build1 [10.9 kB] Get:18 http://ftpmaster.internal/ubuntu disco/main amd64 libaudit1 amd64 1:2.8.3-1ubuntu3 [38.8 kB] Get:19 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libkmod2 amd64 25-1ubuntu1.1 [41.8 kB] Get:20 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 systemd amd64 239-7ubuntu10.1 [2968 kB] Get:21 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libsystemd0 amd64 239-7ubuntu10.1 [211 kB] Get:22 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 init amd64 1.55 [6480 B] Get:23 http://ftpmaster.internal/ubuntu disco/main amd64 libquadmath0 amd64 8.2.0-9ubuntu1 [134 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main amd64 libubsan1 amd64 8.2.0-9ubuntu1 [121 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main amd64 libitm1 amd64 8.2.0-9ubuntu1 [28.1 kB] Get:26 http://ftpmaster.internal/ubuntu disco/main amd64 libasan5 amd64 8.2.0-9ubuntu1 [364 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main amd64 gcc-8-base amd64 8.2.0-9ubuntu1 [18.6 kB] Get:28 http://ftpmaster.internal/ubuntu disco/main amd64 libstdc++6 amd64 8.2.0-9ubuntu1 [399 kB] Get:29 http://ftpmaster.internal/ubuntu disco/main amd64 libgomp1 amd64 8.2.0-9ubuntu1 [76.4 kB] Get:30 http://ftpmaster.internal/ubuntu disco/main amd64 libatomic1 amd64 8.2.0-9ubuntu1 [9076 B] Get:31 http://ftpmaster.internal/ubuntu disco/main amd64 liblsan0 amd64 8.2.0-9ubuntu1 [132 kB] Get:32 http://ftpmaster.internal/ubuntu disco/main amd64 libtsan0 amd64 8.2.0-9ubuntu1 [288 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main amd64 libmpx2 amd64 8.2.0-9ubuntu1 [11.7 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main amd64 cpp-8 amd64 8.2.0-9ubuntu1 [7222 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main amd64 libcc1-0 amd64 8.2.0-9ubuntu1 [39.5 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main amd64 gcc-8 amd64 8.2.0-9ubuntu1 [7999 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main amd64 g++-8 amd64 8.2.0-9ubuntu1 [8115 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main amd64 libstdc++-8-dev amd64 8.2.0-9ubuntu1 [1538 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main amd64 libgcc-8-dev amd64 8.2.0-9ubuntu1 [2304 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main amd64 libgcc1 amd64 1:8.2.0-9ubuntu1 [40.7 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main amd64 libbinutils amd64 2.31.1-7ubuntu1 [483 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main amd64 binutils-common amd64 2.31.1-7ubuntu1 [194 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main amd64 binutils amd64 2.31.1-7ubuntu1 [3392 B] Get:44 http://ftpmaster.internal/ubuntu disco/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-7ubuntu1 [1829 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main amd64 libselinux1 amd64 2.8-1build2 [68.6 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main amd64 libsemanage-common all 2.8-1build2 [6892 B] Get:47 http://ftpmaster.internal/ubuntu disco/main amd64 libsemanage1 amd64 2.8-1build2 [85.1 kB] Get:48 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libudev1 amd64 239-7ubuntu10.1 [53.9 kB] Get:49 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libseccomp2 amd64 2.3.3-3ubuntu2 [38.9 kB] Get:50 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libdevmapper1.02.1 amd64 2:1.02.145-4.1ubuntu4 [127 kB] Get:51 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 dmsetup amd64 2:1.02.145-4.1ubuntu4 [74.6 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main amd64 tzdata all 2018g-1 [188 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main amd64 g++ amd64 4:8.2.0-2ubuntu2 [1608 B] Get:54 http://ftpmaster.internal/ubuntu disco/main amd64 gcc amd64 4:8.2.0-2ubuntu2 [5224 B] Get:55 http://ftpmaster.internal/ubuntu disco/main amd64 cpp amd64 4:8.2.0-2ubuntu2 [27.6 kB] Get:56 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 linux-libc-dev amd64 4.18.0-11.12 [1039 kB] Get:57 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 lockfile-progs amd64 0.1.18 [9872 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 46.1 MB in 2s (25.0 MB/s) (Reading database ... 12650 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu8_amd64.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 ... 12650 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-1_amd64.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) ... 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Setting up libdevmapper1.02.1:amd64 (2:1.02.145-4.1ubuntu4) ... Setting up liblsan0:amd64 (8.2.0-9ubuntu1) ... Setting up libgdbm6:amd64 (1.18.1-1) ... Setting up binutils-common:amd64 (2.31.1-7ubuntu1) ... Setting up libmpx2:amd64 (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:amd64 (1.18.1-1) ... Setting up lockfile-progs (0.1.18) ... Setting up libasan5:amd64 (8.2.0-9ubuntu1) ... Setting up libitm1:amd64 (8.2.0-9ubuntu1) ... Setting up libubsan1:amd64 (8.2.0-9ubuntu1) ... Setting up libbinutils:amd64 (2.31.1-7ubuntu1) ... Setting up libperl5.28:amd64 (5.28.0-3) ... Setting up perl (5.28.0-3) ... Setting up libgcc-8-dev:amd64 (8.2.0-9ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.31.1-7ubuntu1) ... Setting up libstdc++-8-dev:amd64 (8.2.0-9ubuntu1) ... Setting up binutils (2.31.1-7ubuntu1) ... 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-15626188 amd64 disco-proposed -c chroot:build-PACKAGEBUILD-15626188 --arch=amd64 --dist=disco-proposed --nolog -A consensuscore_1.1.1+dfsg-1.dsc Initiating build PACKAGEBUILD-15626188 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 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-012.buildd +==============================================================================+ | consensuscore 1.1.1+dfsg-1 (amd64) 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: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/consensuscore-qaZiyL/consensuscore-1.1.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/consensuscore-qaZiyL' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15626188/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-5VXTBq/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-5VXTBq/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5VXTBq/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-5VXTBq/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5VXTBq/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-5VXTBq/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (158 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-5VXTBq/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 ... 14539 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 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-EYiBOS/apt_archive/sbuild-build-depends-consensuscore-dummy.deb'. Ign:1 copy:/<>/resolver-EYiBOS/apt_archive ./ InRelease Get:2 copy:/<>/resolver-EYiBOS/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-EYiBOS/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-EYiBOS/apt_archive ./ Sources [274 B] Get:5 copy:/<>/resolver-EYiBOS/apt_archive ./ Packages [595 B] Fetched 2988 B in 0s (168 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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amd64 python2.7-dev amd64 2.7.15-4ubuntu4 [280 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main amd64 python2-dev amd64 2.7.15-3 [1240 B] Get:74 http://ftpmaster.internal/ubuntu disco/main amd64 python-dev amd64 2.7.15-3 [1220 B] Get:75 http://ftpmaster.internal/ubuntu disco/main amd64 python-all-dev amd64 2.7.15-3 [1096 B] Get:76 http://ftpmaster.internal/ubuntu disco/main amd64 python-numpy amd64 1:1.14.5-1ubuntu7 [2016 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main amd64 python-pkg-resources all 40.5.0-1 [129 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main amd64 python-setuptools all 40.5.0-1 [324 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main amd64 python3-all amd64 3.7.1-1ubuntu1 [1108 B] Get:80 http://ftpmaster.internal/ubuntu disco/main amd64 python3.7-dev amd64 3.7.1-1 [521 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main amd64 python3-dev amd64 3.7.1-1ubuntu1 [1308 B] Get:82 http://ftpmaster.internal/ubuntu disco/main amd64 python3-all-dev amd64 3.7.1-1ubuntu1 [1112 B] Get:83 http://ftpmaster.internal/ubuntu disco/main amd64 python3-numpy amd64 1:1.14.5-1ubuntu7 [2027 kB] Get:84 http://ftpmaster.internal/ubuntu disco/main amd64 python3-pkg-resources all 40.5.0-1 [99.6 kB] Get:85 http://ftpmaster.internal/ubuntu disco/main amd64 python3-setuptools all 40.5.0-1 [249 kB] Get:86 http://ftpmaster.internal/ubuntu disco/universe amd64 swig3.0 amd64 3.0.12-1.2 [1098 kB] Get:87 http://ftpmaster.internal/ubuntu disco/universe amd64 swig amd64 3.0.12-1.2 [6464 B] Get:88 http://ftpmaster.internal/ubuntu disco/main amd64 dh-exec amd64 0.23build1 [24.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 126 MB in 7s (19.2 MB/s) Selecting previously unselected package libpython3.7-minimal:amd64. 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Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgfortran5:amd64 (8.2.0-9ubuntu1) ... Setting up libpython2.7-stdlib:amd64 (2.7.15-4ubuntu4) ... Setting up autopoint (0.19.8.1-8) ... Setting up libmpdec2:amd64 (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:amd64 (3.7.1-1) ... Setting up gettext (0.19.8.1-8) ... Setting up liblapack3:amd64 (3.8.0-1build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-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) ... 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Setting up libpython2-dev:amd64 (2.7.15-3) ... Setting up libpython-stdlib:amd64 (2.7.15-3) ... Setting up libpython3-all-dev:amd64 (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:amd64 (2.7.15-3) ... Setting up python-dev (2.7.15-3) ... Setting up libpython-all-dev:amd64 (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 (x86_64) 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-x86-64-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 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+------------------------------------------------------------------------------+ | 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-15626188 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15626188 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15626188 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 amd64 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-amd64' 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-amd64' 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 dh build --with python2,python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -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 -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++/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 -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 -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++/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++/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++/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 -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 -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 -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 -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/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 -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 -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/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++/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 -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++/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 -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 -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 -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++/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++/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++/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++/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++/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 (1 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (0 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (1 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (0 ms) [----------] 4 tests from PoaGraph (2 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (0 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (0 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (1 ms) [ RUN ] PoaConsensus.SmallTilingTest [ OK ] PoaConsensus.SmallTilingTest (0 ms) [ RUN ] PoaConsensus.TestVerboseGraphVizOutput [ OK ] PoaConsensus.TestVerboseGraphVizOutput (0 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png sh: 1: dot: not found [ OK ] PoaConsensus.TestLocalStaggered (8 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (1 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (1225 ms) [----------] 8 tests from PoaConsensus (1236 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (130 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (137 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (151 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (108 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (10 ms) [----------] 5 tests from QvEvaluatorTest (537 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 (4 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (2 ms) [----------] 8 tests from MutationScorerTest/0 (7 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 (1 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 (4 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (2 ms) [----------] 8 tests from MutationScorerTest/1 (7 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 (1 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 (3 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (2 ms) [----------] 8 tests from MutationScorerTest/2 (8 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 (4 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest [ OK ] MutationScorerTest/3.DinucleotideDeletionTest (2 ms) [----------] 8 tests from MutationScorerTest/3 (7 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 (1 ms) [ RUN ] RecursorTest/0.ExtendBetaTest [ OK ] RecursorTest/0.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/0 (3 ms total) [----------] 7 tests from RecursorTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/1.SmallMatchTest [ OK ] RecursorTest/1.SmallMatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMismatchTest [ OK ] RecursorTest/1.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/1.SmallMergeTest [ OK ] RecursorTest/1.SmallMergeTest (0 ms) [ RUN ] RecursorTest/1.MediumSizedTest [ OK ] RecursorTest/1.MediumSizedTest (6 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 (6 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 (5 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (1 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 (7 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 (1 ms) [ RUN ] RecursorTest/3.MediumSizedTest [ OK ] RecursorTest/3.MediumSizedTest (5 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (1 ms) [----------] 7 tests from RecursorTest/3 (7 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (39 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (41 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (42 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (67 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (67 ms) [----------] 5 tests from RecursorFuzzTest/0 (256 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (126 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (128 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (123 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (73 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (73 ms) [----------] 5 tests from RecursorFuzzTest/1 (523 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (189 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (192 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (204 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (57 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (54 ms) [----------] 5 tests from RecursorFuzzTest/2 (696 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (146 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (142 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (140 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (53 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (55 ms) [----------] 5 tests from RecursorFuzzTest/3 (537 ms total) [----------] 3 tests from CoverageTests [ RUN ] CoverageTests.CoverageInWindowTest [ OK ] CoverageTests.CoverageInWindowTest (1 ms) [ RUN ] CoverageTests.CoveredIntervalsTest [ OK ] CoverageTests.CoveredIntervalsTest (0 ms) [ RUN ] CoverageTests.CoveredIntervalsTest2 [ OK ] CoverageTests.CoveredIntervalsTest2 (0 ms) [----------] 3 tests from CoverageTests (1 ms total) [----------] 3 tests from PairwiseAlignmentTests [ RUN ] PairwiseAlignmentTests.RepresentationTests [ OK ] PairwiseAlignmentTests.RepresentationTests (0 ms) [ RUN ] PairwiseAlignmentTests.GlobalAlignmentTests [ OK ] PairwiseAlignmentTests.GlobalAlignmentTests (0 ms) [ RUN ] PairwiseAlignmentTests.TargetPositionsInQueryTest [ OK ] PairwiseAlignmentTests.TargetPositionsInQueryTest (0 ms) [----------] 3 tests from PairwiseAlignmentTests (0 ms total) [----------] 2 tests from AffineAlignmentTests [ RUN ] AffineAlignmentTests.BasicTests [ OK ] AffineAlignmentTests.BasicTests (0 ms) [ RUN ] AffineAlignmentTests.LargeGapTest [ OK ] AffineAlignmentTests.LargeGapTest (23 ms) [----------] 2 tests from AffineAlignmentTests (23 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 (0 ms total) [----------] 1 test from QuiverConfigTableTests [ RUN ] QuiverConfigTableTests.IllegalChemistry [ OK ] QuiverConfigTableTests.IllegalChemistry (1 ms) [----------] 1 test from QuiverConfigTableTests (1 ms total) [----------] 3 tests from MutationOrientationTests [ RUN ] MutationOrientationTests.ReadScoresMutation1 [ OK ] MutationOrientationTests.ReadScoresMutation1 (0 ms) [ RUN ] MutationOrientationTests.ReadScoresMutation2 [ OK ] MutationOrientationTests.ReadScoresMutation2 (0 ms) [ RUN ] MutationOrientationTests.OrientedMutation [ OK ] MutationOrientationTests.OrientedMutation (0 ms) [----------] 3 tests from MutationOrientationTests (0 ms total) [----------] 11 tests from MultiReadMutationScorerTest/0, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MultiReadMutationScorerTest/0.Template [ OK ] MultiReadMutationScorerTest/0.Template (0 ms) [ RUN ] MultiReadMutationScorerTest/0.BasicTest [ OK ] MultiReadMutationScorerTest/0.BasicTest (2 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest [ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (3 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest [ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (2 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (1 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 (1 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms) [----------] 11 tests from MultiReadMutationScorerTest/0 (11 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 (4 ms) [ RUN ] MutationEnumerationTest.TestDinucleotideMutations [ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) [----------] 4 tests from MutationEnumerationTest (4 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 (19 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 (20 ms total) [----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix [ RUN ] MatrixTest/1.Basic [ OK ] MatrixTest/1.Basic (0 ms) [ RUN ] MatrixTest/1.Nullability [ OK ] MatrixTest/1.Nullability (0 ms) [ RUN ] MatrixTest/1.Ranges [ OK ] MatrixTest/1.Ranges (0 ms) [ RUN ] MatrixTest/1.IsColumnEmpty [ OK ] MatrixTest/1.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/1.SSE [ OK ] MatrixTest/1.SSE (0 ms) [ RUN ] MatrixTest/1.ToHostArray [ OK ] MatrixTest/1.ToHostArray (0 ms) [ RUN ] MatrixTest/1.NonSequentialAccess [ OK ] MatrixTest/1.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/1.Holes [ OK ] MatrixTest/1.Holes (0 ms) [ RUN ] MatrixTest/1.BigBandedMatrix N13ConsensusCore12SparseMatrixE : 1001976 [ OK ] MatrixTest/1.BigBandedMatrix (11 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. (3915 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 dh binary --with python2,python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -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 -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -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.x86_64-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-x86_64-linux-gnu.so dh_numpy3 make[1]: Leaving directory '/<>/consensuscore-1.1.1+dfsg' dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-pbconsensuscore/usr/lib/python2.7/dist-packages/_ConsensusCore.x86_64-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-pbconsensuscore/usr/lib/python3/dist-packages/_ConsensusCore.cpython-37m-x86_64-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package libconsensuscore-dev: unknown substitution variable ${shlibs:Depends} dpkg-gencontrol: warning: package libconsensuscore-dev: unused substitution variable ${python3:Depends} dpkg-gencontrol: warning: package libconsensuscore-dev: unused substitution variable ${python:Depends} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python3:Versions} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python:Depends} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python3:Depends} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python:Versions} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python3:Provides} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python3:Versions} dpkg-gencontrol: warning: package python3-pbconsensuscore: unused substitution variable ${python:Depends} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python3:Depends} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python:Provides} dpkg-gencontrol: warning: package python-pbconsensuscore: unused substitution variable ${python:Versions} dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 INFO: pkgstriptranslations version 143 pkgstriptranslations: processing libconsensuscore-dev (in debian/libconsensuscore-dev); do_strip: , oemstrip: pkgstriptranslations: processing python3-pbconsensuscore-dbgsym (in debian/.debhelper/python3-pbconsensuscore/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing python-pbconsensuscore-dbgsym (in debian/.debhelper/python-pbconsensuscore/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libconsensuscore-dev/DEBIAN/control, package libconsensuscore-dev, directory debian/libconsensuscore-dev pkgstripfiles: Running PNG optimization (using 4 cpus) for package libconsensuscore-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-1_amd64.deb'. 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_amd64.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_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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_amd64.deb'. Renaming python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.deb to python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.ddeb INFO: pkgstriptranslations version 143 pkgstriptranslations: processing python3-pbconsensuscore (in debian/python3-pbconsensuscore); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-pbconsensuscore/DEBIAN/control, package python3-pbconsensuscore, directory debian/python3-pbconsensuscore pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pbconsensuscore ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-1_amd64.deb'. Renaming python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.deb to python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../consensuscore_1.1.1+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build consensuscore-1.1.1+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20181109-0830 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ consensuscore_1.1.1+dfsg-1_amd64.changes: ----------------------------------------- Format: 1.8 Date: Tue, 09 Oct 2018 17:43:54 +0200 Source: consensuscore Binary: libconsensuscore-dev python-pbconsensuscore python3-pbconsensuscore Architecture: amd64 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: d66e6085dc6a2e8ed33932a94169e64df72ce164 7939 consensuscore_1.1.1+dfsg-1_amd64.buildinfo c7fdd59ad12be226cde3f92640b9a93ea78b6547 454760 libconsensuscore-dev_1.1.1+dfsg-1_amd64.deb d533d0c75732c0a9e560e93e400bc8be21007133 9811844 python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.ddeb 74841e67b1b990c5c71ad85ce7c410653456f2a6 664092 python-pbconsensuscore_1.1.1+dfsg-1_amd64.deb 866e0a25a62b3580eb697cb27e239615ae908734 9855104 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.ddeb 3a52d4cda23c8912e8e10f2a06898684394148cc 662992 python3-pbconsensuscore_1.1.1+dfsg-1_amd64.deb Checksums-Sha256: 0df273df615a979afaca6fd5254851b377c63784047827a90db1c8579d38b888 7939 consensuscore_1.1.1+dfsg-1_amd64.buildinfo 77bdd3cf1fb8fc7c59a7c1ed627152abff759f29b4ac6b874120ffc5f00c3962 454760 libconsensuscore-dev_1.1.1+dfsg-1_amd64.deb 8fb641be23530ec1ec26d376f667a2d18fd1f15af2bfe67b96e0c346b292b880 9811844 python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.ddeb a7334fb4e109d99e7f4ff0a4b484cba025846c87d7721321975ba812ded5e45c 664092 python-pbconsensuscore_1.1.1+dfsg-1_amd64.deb 5fe5011ee4a0d768ed969058d704b7d481bf60046c3c86e230f41229fc077c01 9855104 python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.ddeb 286dec09c546bcf0b2b9921902f30e80fcc9f67286cfea7427194653d4644e16 662992 python3-pbconsensuscore_1.1.1+dfsg-1_amd64.deb Files: 6492f6f0b8b53025a14d791f29a67e01 7939 science optional consensuscore_1.1.1+dfsg-1_amd64.buildinfo 95a4caa58eac629809896a115f600c78 454760 libdevel optional libconsensuscore-dev_1.1.1+dfsg-1_amd64.deb cb059b9eb38e76e455b5ed3a87058c87 9811844 debug optional python-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.ddeb b3bd07e54cfd8818785fd1dadc8cb2f6 664092 python optional python-pbconsensuscore_1.1.1+dfsg-1_amd64.deb 2771c247263c7489c2ae5be3dd5be93f 9855104 debug optional python3-pbconsensuscore-dbgsym_1.1.1+dfsg-1_amd64.ddeb edabd6489c3cc045ee0e8552cc199e69 662992 python optional python3-pbconsensuscore_1.1.1+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libconsensuscore-dev_1.1.1+dfsg-1_amd64.deb ------------------------------------------- new debian package, version 2.0. size 454760 bytes: control archive=2224 bytes. 813 bytes, 18 lines control 4297 bytes, 53 lines md5sums Package: libconsensuscore-dev Source: consensuscore Version: 1.1.1+dfsg-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3754 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_amd64.deb --------------------------------------------- new debian package, version 2.0. size 664092 bytes: control archive=1296 bytes. 980 bytes, 19 lines control 685 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: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2947 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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