Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/c/consensuscore/consensuscore_1.1.1+dfsg-2+b3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/consensuscore-1.1.1+dfsg-2+b3l019upc1/consensuscore_1.1.1+dfsg-2+b3_amd64.buildinfo Get source package info: consensuscore=1.1.1+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/consensuscore/1.1.1+dfsg-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.3-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc3-1 binutils=2.35.1-4 binutils-common=2.35.1-4 binutils-x86-64-linux-gnu=2.35.1-4 bsdextrautils=2.36.1-2 bsdutils=1:2.36.1-2 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-23 dash=0.5.11+git20200708+dd9ef66-2 debconf=1.5.74 debhelper=13.3 debianutils=4.11.2 dh-autoreconf=19 dh-exec=0.23.2 dh-python=4.20201102 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13+20201015-2 file=1:5.39-3 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-23 gcc=4:10.2.0-1 gcc-10=10.2.0-23 gcc-10-base=10.2.0-23 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.59 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-23 libatomic1=10.2.0-23 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbinutils=2.35.1-4 libblas3=3.9.0-3 libblkid1=2.36.1-2 libboost-dev=1.71.0.3 libboost1.71-dev=1.71.0-7+b1 libbz2-1.0=1.0.8-4 libc-bin=2.31-5 libc-dev-bin=2.31-5 libc6=2.31-5 libc6-dev=2.31-5 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.0-23 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-4 libctf0=2.35.1-4 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.3 libdpkg-perl=1.20.5 libelf1=0.182-1 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-23 libgcc-s1=10.2.0-23 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgfortran5=10.2.0-23 libglib2.0-0=2.66.3-2 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.0-23 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libicu67=67.1-4 libisl23=0.23-1 libitm1=10.2.0-23 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblapack3=3.9.0-3 liblsan0=10.2.0-23 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.35-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-5 libpipeline1=1.5.3-1 libpython3-all-dev=3.9.0-4 libpython3-dev=3.9.0-4 libpython3-stdlib=3.9.0-4 libpython3.8-minimal=3.8.6-1 libpython3.8-stdlib=3.8.6-1 libpython3.9=3.9.1~rc1-2 libpython3.9-dev=3.9.1~rc1-2 libpython3.9-minimal=3.9.1~rc1-2 libpython3.9-stdlib=3.9.1~rc1-2 libquadmath0=10.2.0-23 libreadline8=8.1~rc3-1 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsmartcols1=2.36.1-2 libsqlite3-0=3.34.0-1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-23 libstdc++6=10.2.0-23 libsub-override-perl=0.09-2 libsystemd0=247.1-3 libtinfo6=6.2+20201114-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.0-23 libubsan1=10.2.0-23 libuchardet0=0.0.7-1 libudev1=247.1-3 libunistring2=0.9.10-4 libuuid1=2.36.1-2 libxml2=2.9.10+dfsg-6.3 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.11-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 mailcap=3.67 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=1.0.1 mime-support=3.66 ncurses-base=6.2+20201114-1 ncurses-bin=6.2+20201114-1 patch=2.7.6-6 perl=5.32.0-5 perl-base=5.32.0-5 perl-modules-5.32=5.32.0-5 po-debconf=1.0.21 python3=3.9.0-4 python3-all=3.9.0-4 python3-all-dev=3.9.0-4 python3-dev=3.9.0-4 python3-distutils=3.8.6-1 python3-lib2to3=3.8.6-1 python3-minimal=3.9.0-4 python3-numpy=1:1.19.4-1 python3-pkg-resources=50.3.0-1 python3-setuptools=50.3.0-1 python3.8=3.8.6-1 python3.8-minimal=3.8.6-1 python3.9=3.9.1~rc1-2 python3.9-dev=3.9.1~rc1-2 python3.9-minimal=3.9.1~rc1-2 readline-common=8.1~rc3-1 sed=4.7-1 sensible-utils=0.0.12+nmu1 swig=4.0.2-1 swig4.0=4.0.2-1 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 tzdata=2020d-1 util-linux=2.36.1-2 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201207T144442Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d consensuscore=1.1.1+dfsg-2 && mkdir -p /build/consensuscore-ZVmnDX && dpkg-source --no-check -x /*.dsc /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg && cd /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg && { printf '%s' 'consensuscore (1.1.1+dfsg-2+b3) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Python 3.9 only -- all / amd64 / i386 Build Daemon (x86-conova-01) Mon, 07 Dec 2020 13:14:56 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/consensuscore-ZVmnDX" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607346896" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/consensuscore-ZVmnDX /tmp/consensuscore-1.1.1+dfsg-2+b3l019upc1 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201207T144442Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.UDld6HBi3D as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.UDld6HBi3D Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-2). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20201207T144442Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201207T144442Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1054 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4614 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-5) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201207T144442Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.UDld6HBi3D Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20201207T144442Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 19s (1166 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.UDld6HBi3D I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d consensuscore=1.1.1+dfsg-2 && mkdir -p /build/consensuscore-ZVmnDX && dpkg-source --no-check -x /*.dsc /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg && cd /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg && { printf '%s' 'consensuscore (1.1.1+dfsg-2+b3) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Python 3.9 only -- all / amd64 / i386 Build Daemon (x86-conova-01) Mon, 07 Dec 2020 13:14:56 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/consensuscore-ZVmnDX"' exec /tmp/mmdebstrap.UDld6HBi3D Reading package lists... NOTICE: 'consensuscore' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/consensuscore.git Please use: git clone https://salsa.debian.org/med-team/consensuscore.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 375 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main consensuscore 1.1.1+dfsg-2 (dsc) [2308 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main consensuscore 1.1.1+dfsg-2 (tar) [364 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main consensuscore 1.1.1+dfsg-2 (diff) [8468 B] Fetched 375 kB in 0s (999 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'consensuscore_1.1.1+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting consensuscore in /build/consensuscore-ZVmnDX/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-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling.patch dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying check_boost_version.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1607346896" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.UDld6HBi3D dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-2+b3 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by all / amd64 / i386 Build Daemon (x86-conova-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py clean WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build-arch dh build-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:232: /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/swig4.0 PYTHON_INCLUDE = /usr/include/python3.9 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Mutation.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConsensus.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/detail/RecursorBase.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SseRecursor.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SimpleRecursor.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o src/C++/Quiver/MutationScorer.cpp: In instantiation of ‘ConsensusCore::MutationScorer::MutationScorer(const EvaluatorType&, const R&) [with R = ConsensusCore::SimpleRecursor; ConsensusCore::MutationScorer::EvaluatorType = ConsensusCore::QvEvaluator]’: src/C++/Quiver/MutationScorer.cpp:190:16: required from here src/C++/Quiver/MutationScorer.cpp:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] 30 | } 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:30:41: 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:30:41: 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:30:41: 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:30:41: 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:30:41: 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:30:41: warning: catching polymorphic type ‘class ConsensusCore::AlphaBetaMismatchException’ by value [-Wcatch-value=] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Diploid.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Diploid.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Statistics/Binomial.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Binomial.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Utils.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Feature.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Utils.o -MM src/C++/Utils.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Utils.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/PairwiseAlignment.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Feature.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Read.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Read.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Features.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Features.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Coverage.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Binomial.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Version.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Version.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Edna/EdnaCounts.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Coverage.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Sequence.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Sequence.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Logging.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Features.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Logging.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/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/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraph.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Version.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Checksum.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d ar crs /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Version.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o touch /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a make[2]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/consensuscore-ZVmnDX/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=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.9 -I /usr/lib/python3/dist-packages/numpy/core/include /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' /usr/bin/make test make[2]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' /usr/bin/make -f make/Cpp.mk -j8 make[3]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make[3]: '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[3]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make[3]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestCoverage.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestMutations.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestMutationEnumerator.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestSparseVector.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestDiploidQuiver.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestRecursors.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestPairwiseAlignment.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestMatrixFacades.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestMutationScorer.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestPoaConsensus.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestQvEvaluator.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/ParameterSettings.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 -c /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/src/Tests/TestMultiReadMutationScorer.cpp -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestCoverage.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestMutations.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestMutationEnumerator.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestSparseVector.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestDiploidQuiver.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestRecursors.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestPairwiseAlignment.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestMatrixFacades.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestMutationScorer.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestPoaConsensus.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestQvEvaluator.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/ParameterSettings.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/TestMultiReadMutationScorer.o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0 /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock-gtest-all.cc /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external/gmock-1.7.0/gmock_main.cc -lpthread -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Tests/test-runner GTEST_OUTPUT="xml:tests-summary.xml" /build/consensuscore-ZVmnDX/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. [----------] 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) [----------] 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) [----------] 4 tests from MutationEnumerationTest [ RUN ] MutationEnumerationTest.TestAllMutations [ OK ] MutationEnumerationTest.TestAllMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueMutations [ OK ] MutationEnumerationTest.TestUniqueMutations (0 ms) [ RUN ] MutationEnumerationTest.TestUniqueNearbyMutations [ OK ] MutationEnumerationTest.TestUniqueNearbyMutations (3 ms) [ RUN ] MutationEnumerationTest.TestDinucleotideMutations [ OK ] MutationEnumerationTest.TestDinucleotideMutations (0 ms) [----------] 4 tests from MutationEnumerationTest (3 ms total) [----------] 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) [----------] 7 tests from RecursorTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorTest/0.SmallMatchTest [ OK ] RecursorTest/0.SmallMatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMismatchTest [ OK ] RecursorTest/0.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/0.SmallMergeTest [ OK ] RecursorTest/0.SmallMergeTest (0 ms) [ RUN ] RecursorTest/0.MediumSizedTest [ OK ] RecursorTest/0.MediumSizedTest (1 ms) [ RUN ] RecursorTest/0.LinkTest [ OK ] RecursorTest/0.LinkTest (0 ms) [ RUN ] RecursorTest/0.ExtendAlphaTest [ OK ] RecursorTest/0.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/0.ExtendBetaTest [ OK ] RecursorTest/0.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/0 (1 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 (43 ms) [ RUN ] RecursorTest/1.LinkTest [ OK ] RecursorTest/1.LinkTest (1 ms) [ RUN ] RecursorTest/1.ExtendAlphaTest [ OK ] RecursorTest/1.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/1.ExtendBetaTest [ OK ] RecursorTest/1.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/1 (44 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 (3 ms) [ RUN ] RecursorTest/2.LinkTest [ OK ] RecursorTest/2.LinkTest (0 ms) [ RUN ] RecursorTest/2.ExtendAlphaTest [ OK ] RecursorTest/2.ExtendAlphaTest (1 ms) [ RUN ] RecursorTest/2.ExtendBetaTest [ OK ] RecursorTest/2.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/2 (4 ms total) [----------] 7 tests from RecursorTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorTest/3.SmallMatchTest [ OK ] RecursorTest/3.SmallMatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMismatchTest [ OK ] RecursorTest/3.SmallMismatchTest (0 ms) [ RUN ] RecursorTest/3.SmallMergeTest [ OK ] RecursorTest/3.SmallMergeTest (0 ms) [ RUN ] RecursorTest/3.MediumSizedTest [ OK ] RecursorTest/3.MediumSizedTest (3 ms) [ RUN ] RecursorTest/3.LinkTest [ OK ] RecursorTest/3.LinkTest (0 ms) [ RUN ] RecursorTest/3.ExtendAlphaTest [ OK ] RecursorTest/3.ExtendAlphaTest (0 ms) [ RUN ] RecursorTest/3.ExtendBetaTest [ OK ] RecursorTest/3.ExtendBetaTest (0 ms) [----------] 7 tests from RecursorTest/3 (3 ms total) [----------] 5 tests from RecursorFuzzTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/0.AlphaBetaConcordance [ OK ] RecursorFuzzTest/0.AlphaBetaConcordance (27 ms) [ RUN ] RecursorFuzzTest/0.Alignment [ OK ] RecursorFuzzTest/0.Alignment (18 ms) [ RUN ] RecursorFuzzTest/0.LinkAlphaBeta [ OK ] RecursorFuzzTest/0.LinkAlphaBeta (27 ms) [ RUN ] RecursorFuzzTest/0.ExtendAlpha [ OK ] RecursorFuzzTest/0.ExtendAlpha (50 ms) [ RUN ] RecursorFuzzTest/0.ExtendBeta [ OK ] RecursorFuzzTest/0.ExtendBeta (26 ms) [----------] 5 tests from RecursorFuzzTest/0 (148 ms total) [----------] 5 tests from RecursorFuzzTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/1.AlphaBetaConcordance [ OK ] RecursorFuzzTest/1.AlphaBetaConcordance (70 ms) [ RUN ] RecursorFuzzTest/1.Alignment [ OK ] RecursorFuzzTest/1.Alignment (87 ms) [ RUN ] RecursorFuzzTest/1.LinkAlphaBeta [ OK ] RecursorFuzzTest/1.LinkAlphaBeta (84 ms) [ RUN ] RecursorFuzzTest/1.ExtendAlpha [ OK ] RecursorFuzzTest/1.ExtendAlpha (32 ms) [ RUN ] RecursorFuzzTest/1.ExtendBeta [ OK ] RecursorFuzzTest/1.ExtendBeta (23 ms) [----------] 5 tests from RecursorFuzzTest/1 (296 ms total) [----------] 5 tests from RecursorFuzzTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] RecursorFuzzTest/2.AlphaBetaConcordance [ OK ] RecursorFuzzTest/2.AlphaBetaConcordance (97 ms) [ RUN ] RecursorFuzzTest/2.Alignment [ OK ] RecursorFuzzTest/2.Alignment (93 ms) [ RUN ] RecursorFuzzTest/2.LinkAlphaBeta [ OK ] RecursorFuzzTest/2.LinkAlphaBeta (89 ms) [ RUN ] RecursorFuzzTest/2.ExtendAlpha [ OK ] RecursorFuzzTest/2.ExtendAlpha (18 ms) [ RUN ] RecursorFuzzTest/2.ExtendBeta [ OK ] RecursorFuzzTest/2.ExtendBeta (44 ms) [----------] 5 tests from RecursorFuzzTest/2 (341 ms total) [----------] 5 tests from RecursorFuzzTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] RecursorFuzzTest/3.AlphaBetaConcordance [ OK ] RecursorFuzzTest/3.AlphaBetaConcordance (59 ms) [ RUN ] RecursorFuzzTest/3.Alignment [ OK ] RecursorFuzzTest/3.Alignment (84 ms) [ RUN ] RecursorFuzzTest/3.LinkAlphaBeta [ OK ] RecursorFuzzTest/3.LinkAlphaBeta (78 ms) [ RUN ] RecursorFuzzTest/3.ExtendAlpha [ OK ] RecursorFuzzTest/3.ExtendAlpha (17 ms) [ RUN ] RecursorFuzzTest/3.ExtendBeta [ OK ] RecursorFuzzTest/3.ExtendBeta (18 ms) [----------] 5 tests from RecursorFuzzTest/3 (256 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 (33 ms) [----------] 2 tests from AffineAlignmentTests (33 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) [----------] 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 (3 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 (3 ms total) [----------] 11 tests from MatrixTest/1, where TypeParam = ConsensusCore::SparseMatrix [ RUN ] MatrixTest/1.Basic [ OK ] MatrixTest/1.Basic (0 ms) [ RUN ] MatrixTest/1.Nullability [ OK ] MatrixTest/1.Nullability (0 ms) [ RUN ] MatrixTest/1.Ranges [ OK ] MatrixTest/1.Ranges (0 ms) [ RUN ] MatrixTest/1.IsColumnEmpty [ OK ] MatrixTest/1.IsColumnEmpty (0 ms) [ RUN ] MatrixTest/1.SSE [ OK ] MatrixTest/1.SSE (0 ms) [ RUN ] MatrixTest/1.ToHostArray [ OK ] MatrixTest/1.ToHostArray (0 ms) [ RUN ] MatrixTest/1.NonSequentialAccess [ OK ] MatrixTest/1.NonSequentialAccess (0 ms) [ RUN ] MatrixTest/1.Holes [ OK ] MatrixTest/1.Holes (0 ms) [ RUN ] MatrixTest/1.BigBandedMatrix N13ConsensusCore12SparseMatrixE : 1001976 [ OK ] MatrixTest/1.BigBandedMatrix (8 ms) [ RUN ] MatrixTest/1.BigIrregularBandedMatrix [ OK ] MatrixTest/1.BigIrregularBandedMatrix (0 ms) [ RUN ] MatrixTest/1.CopyTest [ OK ] MatrixTest/1.CopyTest (0 ms) [----------] 11 tests from MatrixTest/1 (8 ms total) [----------] 8 tests from MutationScorerTest/0, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/0.BasicTest [ OK ] MutationScorerTest/0.BasicTest (0 ms) [ RUN ] MutationScorerTest/0.CopyTest [ OK ] MutationScorerTest/0.CopyTest (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtBeginning [ OK ] MutationScorerTest/0.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/0.MutationsAtEnd [ OK ] MutationScorerTest/0.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/0.TinyTemplate [ OK ] MutationScorerTest/0.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/0.TemplateMutationWorkflow [ OK ] MutationScorerTest/0.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/0.DinucleotideInsertionTest [ OK ] MutationScorerTest/0.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/0.DinucleotideDeletionTest [ OK ] MutationScorerTest/0.DinucleotideDeletionTest (0 ms) [----------] 8 tests from MutationScorerTest/0 (3 ms total) [----------] 8 tests from MutationScorerTest/1, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/1.BasicTest [ OK ] MutationScorerTest/1.BasicTest (0 ms) [ RUN ] MutationScorerTest/1.CopyTest [ OK ] MutationScorerTest/1.CopyTest (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtBeginning [ OK ] MutationScorerTest/1.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/1.MutationsAtEnd [ OK ] MutationScorerTest/1.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/1.TinyTemplate [ OK ] MutationScorerTest/1.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/1.TemplateMutationWorkflow [ OK ] MutationScorerTest/1.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/1.DinucleotideInsertionTest [ OK ] MutationScorerTest/1.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/1.DinucleotideDeletionTest [ OK ] MutationScorerTest/1.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/1 (3 ms total) [----------] 8 tests from MutationScorerTest/2, where TypeParam = ConsensusCore::SimpleRecursor [ RUN ] MutationScorerTest/2.BasicTest [ OK ] MutationScorerTest/2.BasicTest (0 ms) [ RUN ] MutationScorerTest/2.CopyTest [ OK ] MutationScorerTest/2.CopyTest (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtBeginning [ OK ] MutationScorerTest/2.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/2.MutationsAtEnd [ OK ] MutationScorerTest/2.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/2.TinyTemplate [ OK ] MutationScorerTest/2.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/2.TemplateMutationWorkflow [ OK ] MutationScorerTest/2.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/2.DinucleotideInsertionTest [ OK ] MutationScorerTest/2.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/2.DinucleotideDeletionTest [ OK ] MutationScorerTest/2.DinucleotideDeletionTest (1 ms) [----------] 8 tests from MutationScorerTest/2 (3 ms total) [----------] 8 tests from MutationScorerTest/3, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MutationScorerTest/3.BasicTest [ OK ] MutationScorerTest/3.BasicTest (0 ms) [ RUN ] MutationScorerTest/3.CopyTest [ OK ] MutationScorerTest/3.CopyTest (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtBeginning [ OK ] MutationScorerTest/3.MutationsAtBeginning (0 ms) [ RUN ] MutationScorerTest/3.MutationsAtEnd [ OK ] MutationScorerTest/3.MutationsAtEnd (0 ms) [ RUN ] MutationScorerTest/3.TinyTemplate [ OK ] MutationScorerTest/3.TinyTemplate (0 ms) [ RUN ] MutationScorerTest/3.TemplateMutationWorkflow [ OK ] MutationScorerTest/3.TemplateMutationWorkflow (0 ms) [ RUN ] MutationScorerTest/3.DinucleotideInsertionTest [ OK ] MutationScorerTest/3.DinucleotideInsertionTest (2 ms) [ RUN ] MutationScorerTest/3.DinucleotideDeletionTest [ OK ] MutationScorerTest/3.DinucleotideDeletionTest (0 ms) [----------] 8 tests from MutationScorerTest/3 (2 ms total) [----------] 4 tests from PoaGraph [ RUN ] PoaGraph.SmallBasicTest [ OK ] PoaGraph.SmallBasicTest (1 ms) [ RUN ] PoaGraph.SmallExtraTests [ OK ] PoaGraph.SmallExtraTests (0 ms) [ RUN ] PoaGraph.SmallMismatchTests [ OK ] PoaGraph.SmallMismatchTests (1 ms) [ RUN ] PoaGraph.SmallDeletionTests [ OK ] PoaGraph.SmallDeletionTests (0 ms) [----------] 4 tests from PoaGraph (2 ms total) [----------] 8 tests from PoaConsensus [ RUN ] PoaConsensus.TestSimple [ OK ] PoaConsensus.TestSimple (1 ms) [ RUN ] PoaConsensus.TestOverhangSecond [ OK ] PoaConsensus.TestOverhangSecond (0 ms) [ RUN ] PoaConsensus.SmallSemiglobalTest [ OK ] PoaConsensus.SmallSemiglobalTest (0 ms) [ RUN ] PoaConsensus.SmallTilingTest [ OK ] PoaConsensus.SmallTilingTest (0 ms) [ RUN ] PoaConsensus.TestVerboseGraphVizOutput [ OK ] PoaConsensus.TestVerboseGraphVizOutput (1 ms) [ RUN ] PoaConsensus.TestLocalStaggered dot -Tpng local-staggered.dot > local-staggered.png sh: 1: dot: not found [ OK ] PoaConsensus.TestLocalStaggered (6 ms) [ RUN ] PoaConsensus.TestLongInsert [ OK ] PoaConsensus.TestLongInsert (1 ms) [ RUN ] PoaConsensus.NondeterminismRegressionTest [ OK ] PoaConsensus.NondeterminismRegressionTest (1115 ms) [----------] 8 tests from PoaConsensus (1124 ms total) [----------] 5 tests from QvEvaluatorTest [ RUN ] QvEvaluatorTest.IncVsInc4 [ OK ] QvEvaluatorTest.IncVsInc4 (73 ms) [ RUN ] QvEvaluatorTest.DelVsDel4 [ OK ] QvEvaluatorTest.DelVsDel4 (82 ms) [ RUN ] QvEvaluatorTest.ExtraVsExtra4 [ OK ] QvEvaluatorTest.ExtraVsExtra4 (102 ms) [ RUN ] QvEvaluatorTest.MergeVsMerge4 [ OK ] QvEvaluatorTest.MergeVsMerge4 (53 ms) [ RUN ] QvEvaluatorTest.BadTagTest [ OK ] QvEvaluatorTest.BadTagTest (4 ms) [----------] 5 tests from QvEvaluatorTest (314 ms total) [----------] 1 test from QuiverConfigTableTests [ RUN ] QuiverConfigTableTests.IllegalChemistry [ OK ] QuiverConfigTableTests.IllegalChemistry (0 ms) [----------] 1 test from QuiverConfigTableTests (0 ms total) [----------] 3 tests from MutationOrientationTests [ RUN ] MutationOrientationTests.ReadScoresMutation1 [ OK ] MutationOrientationTests.ReadScoresMutation1 (0 ms) [ RUN ] MutationOrientationTests.ReadScoresMutation2 [ OK ] MutationOrientationTests.ReadScoresMutation2 (0 ms) [ RUN ] MutationOrientationTests.OrientedMutation [ OK ] MutationOrientationTests.OrientedMutation (0 ms) [----------] 3 tests from MutationOrientationTests (0 ms total) [----------] 11 tests from MultiReadMutationScorerTest/0, where TypeParam = ConsensusCore::SseRecursor [ RUN ] MultiReadMutationScorerTest/0.Template [ OK ] MultiReadMutationScorerTest/0.Template (0 ms) [ RUN ] MultiReadMutationScorerTest/0.BasicTest [ OK ] MultiReadMutationScorerTest/0.BasicTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.ManyMutationTest [ OK ] MultiReadMutationScorerTest/0.ManyMutationTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyConstructorTest [ OK ] MultiReadMutationScorerTest/0.CopyConstructorTest (0 ms) [ RUN ] MultiReadMutationScorerTest/0.ReverseStrandTest [ OK ] MultiReadMutationScorerTest/0.ReverseStrandTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtBeginning (0 ms) [ RUN ] MultiReadMutationScorerTest/0.TestMutationsAtEnd [ OK ] MultiReadMutationScorerTest/0.TestMutationsAtEnd (0 ms) [ RUN ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 [ OK ] MultiReadMutationScorerTest/0.NonSpanningReadsTest1 (0 ms) [ RUN ] MultiReadMutationScorerTest/0.CopyTest [ OK ] MultiReadMutationScorerTest/0.CopyTest (1 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseSubstitutionsAtBounds (0 ms) [ RUN ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds [ OK ] MultiReadMutationScorerTest/0.MultiBaseIndelsAtBounds (0 ms) [----------] 11 tests from MultiReadMutationScorerTest/0 (4 ms total) [----------] Global test environment tear-down [==========] 158 tests from 29 test cases ran. (2597 ms total) [ PASSED ] 158 tests. make[3]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make[2]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/consensuscore-ZVmnDX/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/swig4.0 PYTHON_INCLUDE = /usr/include/python3.9 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make[2]: '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' mkdir -p /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/consensuscore-ZVmnDX/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=/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.9 -I /usr/lib/python3/dist-packages/numpy/core/include /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' running install running install_lib running build_py copying build/Python/ConsensusCore.py -> /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build creating /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore creating /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr creating /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib creating /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9 creating /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages copying /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build/ConsensusCore.py -> /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages copying /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build/_ConsensusCore.so -> /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages byte-compiling /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages/ConsensusCore.py to ConsensusCore.cpython-39.pyc running install_egg_info running egg_info creating build/Python/ConsensusCore.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 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 /build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts dh_install -a -O--buildsystem=pybuild dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' dh_python3 I: dh_python3 fs:343: renaming _ConsensusCore.so to _ConsensusCore.cpython-39-x86_64-linux-gnu.so dh_numpy3 make[1]: Leaving directory '/build/consensuscore-ZVmnDX/consensuscore-1.1.1+dfsg' dh_installinit -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-pbconsensuscore/usr/lib/python3/dist-packages/_ConsensusCore.cpython-39-x86_64-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package libconsensuscore-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package libconsensuscore-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-pbconsensuscore: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'libconsensuscore-dev' in '../libconsensuscore-dev_1.1.1+dfsg-2+b3_amd64.deb'. dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-2+b3_amd64.deb'. dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2+b3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../consensuscore_1.1.1+dfsg-2+b3_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/consensuscore-ZVmnDX /tmp/consensuscore-1.1.1+dfsg-2+b3l019upc1 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.UDld6HBi3D... I: success in 1446.3742 seconds md5: Value of 'md5' differs for libconsensuscore-dev_1.1.1+dfsg-2+b3_amd64.deb md5: Size differs for libconsensuscore-dev_1.1.1+dfsg-2+b3_amd64.deb md5: Value of 'md5' differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2+b3_amd64.deb md5: Size differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2+b3_amd64.deb md5: Value of 'md5' differs for python3-pbconsensuscore_1.1.1+dfsg-2+b3_amd64.deb md5: Size differs for python3-pbconsensuscore_1.1.1+dfsg-2+b3_amd64.deb sha1: Value of 'sha1' differs for libconsensuscore-dev_1.1.1+dfsg-2+b3_amd64.deb sha1: Size differs for libconsensuscore-dev_1.1.1+dfsg-2+b3_amd64.deb sha1: Value of 'sha1' differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2+b3_amd64.deb sha1: Size differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2+b3_amd64.deb sha1: Value of 'sha1' differs for python3-pbconsensuscore_1.1.1+dfsg-2+b3_amd64.deb sha1: Size differs for python3-pbconsensuscore_1.1.1+dfsg-2+b3_amd64.deb sha256: Value of 'sha256' differs for libconsensuscore-dev_1.1.1+dfsg-2+b3_amd64.deb sha256: Size differs for libconsensuscore-dev_1.1.1+dfsg-2+b3_amd64.deb sha256: Value of 'sha256' differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2+b3_amd64.deb sha256: Size differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2+b3_amd64.deb sha256: Value of 'sha256' differs for python3-pbconsensuscore_1.1.1+dfsg-2+b3_amd64.deb sha256: Size differs for python3-pbconsensuscore_1.1.1+dfsg-2+b3_amd64.deb Checksums: FAIL diffoscope run passed Cannot generate diffoscope for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-2+b3_amd64.deb: Cannot find URL: http://snapshot.notset.fr/mr/file/6095ddb145f600deac5ead65dc5edfe642bd6177b04ad0988fd1a382e3896062/download diffoscope run passed