Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/c/consensuscore/consensuscore_1.1.1+dfsg-3+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/consensuscore-1.1.1+dfsg-3+b1qesyhnht/consensuscore_1.1.1+dfsg-3+b1_amd64.buildinfo Get source package info: consensuscore=1.1.1+dfsg-3 Source URL: http://snapshot.notset.fr/mr/package/consensuscore/1.1.1+dfsg-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3.1 binutils=2.37-9 binutils-common=2.37-9 binutils-x86-64-linux-gnu=2.37-9 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-exec=0.23.4 dh-python=5.20211114 dh-strip-nondeterminism=1.12.0-2 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-12 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1 libbinutils=2.37-9 libblas3=3.10.0-1 libblkid1=2.37.2-4 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-13 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-9 libctf0=2.37-9 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdpkg-perl=1.20.9 libedit2=3.1-20210910-1 libelf1=0.186-1 libexpat1=2.4.1-3 libexpat1-dev=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.0-2 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran5=11.2.0-12 libgmp10=2:6.2.1+dfsg-3 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libicu67=67.1-7 libisl23=0.24-2 libitm1=11.2.0-12 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-sphinxdoc=4.2.0-5 libjs-underscore=1.9.1~dfsg-4 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblapack3=3.10.0-1 liblsan0=11.2.0-12 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmd0=1.0.4-1 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.3-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libpython3-all-dev=3.9.8-1 libpython3-dev=3.9.8-1 libpython3-stdlib=3.9.8-1 libpython3.10=3.10.0-5 libpython3.10-dev=3.10.0-5 libpython3.10-minimal=3.10.0-5 libpython3.10-stdlib=3.10.0-5 libpython3.9=3.9.9-1 libpython3.9-dev=3.9.9-1 libpython3.9-minimal=3.9.9-1 libpython3.9-stdlib=3.9.9-1 libquadmath0=11.2.0-12 libreadline8=8.1-2 libseccomp2=2.5.2-2 libselinux1=3.3-1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libsqlite3-0=3.36.0-2 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libsub-override-perl=0.09-2 libsystemd0=249.6-2 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.6-2 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libxml2=2.9.12+dfsg-5+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.16-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.70 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.3-1 ncurses-bin=6.3-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 python3=3.9.8-1 python3-all=3.9.8-1 python3-all-dev=3.9.8-1 python3-dev=3.9.8-1 python3-distutils=3.9.9-2 python3-lib2to3=3.9.9-2 python3-minimal=3.9.8-1 python3-numpy=1:1.21.4-2 python3-pkg-resources=58.2.0-1 python3-setuptools=58.2.0-1 python3.10=3.10.0-5 python3.10-dev=3.10.0-5 python3.10-minimal=3.10.0-5 python3.9=3.9.9-1 python3.9-dev=3.9.9-1 python3.9-minimal=3.9.9-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 swig=4.0.2-1 swig4.0=4.0.2-1 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 tzdata=2021e-1 util-linux=2.37.2-4 xz-utils=5.2.5-2 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/20211020T024519Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211020T024519Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211216T085418Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211118T084946Z/ 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-3 && mkdir -p /build/consensuscore-A1AicH && dpkg-source --no-check -x /*.dsc /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg && cd /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg && { printf '%s' 'consensuscore (1.1.1+dfsg-3+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Add Python 3.10 as supported version -- amd64 / i386 Build Daemon (x86-csail-01) Sun, 21 Nov 2021 06:38:41 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/consensuscore-A1AicH" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637476721" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/consensuscore-A1AicH /tmp/consensuscore-1.1.1+dfsg-3+b1qesyhnht bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211118T084946Z 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.UJtRm893zb 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.UJtRm893zb Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). 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/20211118T084946Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1022 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 ... 4669 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... 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/20211020T024519Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211020T024519Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211216T085418Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211118T084946Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.UJtRm893zb Get:1 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm InRelease [128 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211216T085418Z unstable/main amd64 Packages [12.0 MB] Fetched 35.2 MB in 35s (1004 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.UJtRm893zb I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d consensuscore=1.1.1+dfsg-3 && mkdir -p /build/consensuscore-A1AicH && dpkg-source --no-check -x /*.dsc /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg && cd /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg && { printf '%s' 'consensuscore (1.1.1+dfsg-3+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Add Python 3.10 as supported version -- amd64 / i386 Build Daemon (x86-csail-01) Sun, 21 Nov 2021 06:38:41 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/consensuscore-A1AicH"' exec /tmp/mmdebstrap.UJtRm893zb 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/20211020T024519Z bookworm/main consensuscore 1.1.1+dfsg-3 (dsc) [2308 B] Get:2 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm/main consensuscore 1.1.1+dfsg-3 (tar) [364 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211020T024519Z bookworm/main consensuscore 1.1.1+dfsg-3 (diff) [8836 B] Fetched 375 kB in 0s (931 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'consensuscore_1.1.1+dfsg-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting consensuscore in /build/consensuscore-A1AicH/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-3.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-A1AicH/consensuscore-1.1.1+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637476721" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.UJtRm893zb dpkg-buildpackage: info: source package consensuscore dpkg-buildpackage: info: source version 1.1.1+dfsg-3+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-csail-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:237: python3.10 setup.py clean /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/setup.py:4: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.command.build import build as _build /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/setup.py:6: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead from distutils import sysconfig WARNING: '' not a valid package name; please use only .-separated package names in setup.py running clean removing '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.10_pbconsensuscore/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it I: pybuild base:237: 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-A1AicH/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 binary-arch dh binary-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:237: python3.10 setup.py config /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/setup.py:4: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.command.build import build as _build /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/setup.py:6: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead from distutils import sysconfig WARNING: '' not a valid package name; please use only .-separated package names in setup.py running config I: pybuild base:237: 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:237: /usr/bin/python3.10 setup.py build /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/setup.py:4: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.command.build import build as _build /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/setup.py:6: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead from distutils import sysconfig WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig4.0 PYTHON_INCLUDE = /usr/include/python3.10 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' mkdir -p /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AffineAlignment.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/AlignConfig.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/LinearAlignment.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Align/PairwiseAlignment.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Checksum.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Checksum.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Coverage.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Coverage.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Edna/EdnaCounts.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Feature.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Feature.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o -MM src/C++/Align/AlignConfig.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Features.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Features.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Coverage.o -MM src/C++/Coverage.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Coverage.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Logging/Logging.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Logging.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Feature.o -MM src/C++/Feature.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Feature.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/DenseMatrix.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Logging.o -MM src/C++/Logging/Logging.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Logging.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o -MM src/C++/Align/AffineAlignment.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Matrix/SparseMatrix.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Mutation.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Mutation.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o -MM src/C++/Align/LinearAlignment.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaConsensus.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o -MM src/C++/Align/PairwiseAlignment.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Features.o -MM src/C++/Features.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Features.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o -MM src/C++/Edna/EdnaCounts.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o -MM src/C++/Matrix/DenseMatrix.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraph.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o -MM src/C++/Matrix/SparseMatrix.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphImpl.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/PoaGraphTraversals.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Poa/RangeFinder.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/Diploid.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Diploid.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o -MM src/C++/Poa/PoaConsensus.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MultiReadMutationScorer.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Diploid.o -MM src/C++/Quiver/Diploid.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Diploid.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationEnumerator.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o -MM src/C++/Poa/PoaGraph.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/MutationScorer.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Checksum.o -MM src/C++/Checksum.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Checksum.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConfig.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.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 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o -MM src/C++/Quiver/MutationEnumerator.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/QuiverConsensus.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o -MM src/C++/Quiver/QuiverConfig.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/ReadScorer.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o -MM src/C++/Quiver/ReadScorer.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SimpleRecursor.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Mutation.o -MM src/C++/Mutation.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Mutation.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Quiver/SseRecursor.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o -MM src/C++/Poa/RangeFinder.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o -MM src/C++/Poa/PoaGraphTraversals.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Read.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Read.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o -MM src/C++/Quiver/MultiReadMutationScorer.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o -MM src/C++/Quiver/QuiverConsensus.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o -MM src/C++/Quiver/MutationScorer.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o -MM src/C++/Quiver/detail/RecursorBase.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Sequence.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Sequence.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Statistics/Binomial.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Binomial.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Utils.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -c src/C++/Version.cpp -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Version.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Sequence.o -MM src/C++/Sequence.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Sequence.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Utils.o -MM src/C++/Utils.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Utils.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o -MM src/C++/Quiver/SimpleRecursor.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Read.o -MM src/C++/Read.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Read.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Version.o -MM src/C++/Version.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Version.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Binomial.o -MM src/C++/Statistics/Binomial.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Binomial.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o -MM src/C++/Poa/PoaGraphImpl.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.d g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -MT /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o -MM src/C++/Quiver/SseRecursor.cpp > /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.d ar crs /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/AffineAlignment.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/AlignConfig.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/LinearAlignment.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PairwiseAlignment.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Checksum.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Coverage.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/EdnaCounts.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Feature.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Features.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Logging.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/DenseMatrix.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SparseMatrix.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Mutation.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaConsensus.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraph.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraphImpl.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/PoaGraphTraversals.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/RangeFinder.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Diploid.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MultiReadMutationScorer.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MutationEnumerator.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/MutationScorer.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/QuiverConfig.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/QuiverConsensus.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/ReadScorer.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SimpleRecursor.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/SseRecursor.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/RecursorBase.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Read.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Sequence.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Binomial.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Utils.o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/Version.o touch /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a make[2]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' mkdir -p /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/consensuscore-A1AicH/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 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.10 -I /usr/lib/python3/dist-packages/numpy/core/include /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' I: pybuild base:237: /usr/bin/python3 setup.py build WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. 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-A1AicH/consensuscore-1.1.1+dfsg' /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make[2]: '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' mkdir -p /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/consensuscore-A1AicH/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 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.9 -I /usr/lib/python3/dist-packages/numpy/core/include /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3.10 setup.py install --root /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/setup.py:4: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.command.build import build as _build /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/setup.py:6: DeprecationWarning: The distutils.sysconfig module is deprecated, use sysconfig instead from distutils import sysconfig WARNING: '' not a valid package name; please use only .-separated package names in setup.py running build /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. ConsensusCore configuration summary ----------------------------------- BOOST = /usr/include/ SWIG = /usr/bin/swig SWIG_LIB = /usr/share/swig4.0 PYTHON_INCLUDE = /usr/include/python3.10 NUMPY_INCLUDE = /usr/lib/python3/dist-packages/numpy/core/include DEBUG = CPP_STD = c++14 make[1]: Entering directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make[2]: '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' mkdir -p /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/consensuscore-A1AicH/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 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.10 -I /usr/lib/python3/dist-packages/numpy/core/include /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' running install running install_lib running build_py copying build/Python/ConsensusCore.py -> /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.10_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.10_pbconsensuscore/build creating /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore creating /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr creating /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib creating /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.10 creating /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.10/dist-packages copying /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.10_pbconsensuscore/build/ConsensusCore.py -> /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.10/dist-packages copying /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.10_pbconsensuscore/build/_ConsensusCore.so -> /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.10/dist-packages byte-compiling /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.10/dist-packages/ConsensusCore.py to ConsensusCore.cpython-310.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' adding license file 'LICENSES' writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' Copying build/Python/ConsensusCore.egg-info to /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.10/dist-packages/ConsensusCore-1.0.2.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:237: /usr/bin/python3 setup.py install --root /build/consensuscore-A1AicH/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 /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. 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-A1AicH/consensuscore-1.1.1+dfsg' /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. make -f make/Cpp.mk -j8 make[2]: Entering directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make[2]: '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a' is up to date. make[2]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make -f make/Python.mk make[2]: Entering directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' mkdir -p /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python SWIG_LIB=/usr/share/swig4.0 /usr/bin/swig -Wall -c++ -python -builtin -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -module ConsensusCore -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx src/SWIG/ConsensusCore.i /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include/ConsensusCore/Feature.hpp:20: Warning 309: private inheritance from base 'boost::shared_array< T >' (ignored). /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include/ConsensusCore/Matrix/DenseMatrix.hpp:27: Warning 309: private inheritance from base 'boost_dense_matrix' (ignored). /build/consensuscore-A1AicH/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 -ffile-prefix-map=/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DNDEBUG -g -msse3 -fPIC -fno-omit-frame-pointer -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I/usr/include/ -Wl,-z,relro -Wl,-z,now -pthread -shared -Wl,-O1 -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/include -I/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/external -I /usr/include/python3.9 -I /usr/lib/python3/dist-packages/numpy/core/include /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/ConsensusCore_wrap.cxx /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/C++/libConsensusCore.a -o /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/build/Python/_ConsensusCore.so make[2]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' make[1]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' running install running install_lib running build_py copying build/Python/ConsensusCore.py -> /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build copying build/Python/_ConsensusCore.so -> /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build creating /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9 creating /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages copying /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build/ConsensusCore.py -> /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages copying /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/.pybuild/cpython3_3.9_pbconsensuscore/build/_ConsensusCore.so -> /build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg/debian/python3-pbconsensuscore/usr/lib/python3.9/dist-packages byte-compiling /build/consensuscore-A1AicH/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 writing build/Python/ConsensusCore.egg-info/PKG-INFO writing dependency_links to build/Python/ConsensusCore.egg-info/dependency_links.txt writing top-level names to build/Python/ConsensusCore.egg-info/top_level.txt reading manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' adding license file 'LICENSES' writing manifest file 'build/Python/ConsensusCore.egg-info/SOURCES.txt' Copying build/Python/ConsensusCore.egg-info to /build/consensuscore-A1AicH/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-A1AicH/consensuscore-1.1.1+dfsg' dh_python3 I: dh_python3 fs:348: renaming _ConsensusCore.so to _ConsensusCore.cpython-39-x86_64-linux-gnu.so I: dh_python3 fs:348: renaming _ConsensusCore.so to _ConsensusCore.cpython-310-x86_64-linux-gnu.so dh_numpy3 make[1]: Leaving directory '/build/consensuscore-A1AicH/consensuscore-1.1.1+dfsg' 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-310-x86_64-linux-gnu.so debian/python3-pbconsensuscore/usr/lib/python3/dist-packages/_ConsensusCore.cpython-39-x86_64-linux-gnu.so were not linked against libpthread.so.0 (they use 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 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 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-3+b1_amd64.deb'. dpkg-deb: building package 'python3-pbconsensuscore' in '../python3-pbconsensuscore_1.1.1+dfsg-3+b1_amd64.deb'. dpkg-deb: building package 'python3-pbconsensuscore-dbgsym' in '../python3-pbconsensuscore-dbgsym_1.1.1+dfsg-3+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../consensuscore_1.1.1+dfsg-3+b1_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-A1AicH /tmp/consensuscore-1.1.1+dfsg-3+b1qesyhnht I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.UJtRm893zb... I: success in 3307.9566 seconds md5: Value of 'md5' differs for libconsensuscore-dev_1.1.1+dfsg-3+b1_amd64.deb md5: Size differs for libconsensuscore-dev_1.1.1+dfsg-3+b1_amd64.deb md5: Value of 'md5' differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-3+b1_amd64.deb md5: Size differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-3+b1_amd64.deb md5: Value of 'md5' differs for python3-pbconsensuscore_1.1.1+dfsg-3+b1_amd64.deb md5: Size differs for python3-pbconsensuscore_1.1.1+dfsg-3+b1_amd64.deb sha1: Value of 'sha1' differs for libconsensuscore-dev_1.1.1+dfsg-3+b1_amd64.deb sha1: Size differs for libconsensuscore-dev_1.1.1+dfsg-3+b1_amd64.deb sha1: Value of 'sha1' differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-3+b1_amd64.deb sha1: Size differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-3+b1_amd64.deb sha1: Value of 'sha1' differs for python3-pbconsensuscore_1.1.1+dfsg-3+b1_amd64.deb sha1: Size differs for python3-pbconsensuscore_1.1.1+dfsg-3+b1_amd64.deb sha256: Value of 'sha256' differs for libconsensuscore-dev_1.1.1+dfsg-3+b1_amd64.deb sha256: Size differs for libconsensuscore-dev_1.1.1+dfsg-3+b1_amd64.deb sha256: Value of 'sha256' differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-3+b1_amd64.deb sha256: Size differs for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-3+b1_amd64.deb sha256: Value of 'sha256' differs for python3-pbconsensuscore_1.1.1+dfsg-3+b1_amd64.deb sha256: Size differs for python3-pbconsensuscore_1.1.1+dfsg-3+b1_amd64.deb Checksums: FAIL diffoscope run passed Cannot generate diffoscope for python3-pbconsensuscore-dbgsym_1.1.1+dfsg-3+b1_amd64.deb: Cannot find URL: http://snapshot.notset.fr/mr/file/3c00369e00ed061aec2abc21c4b3b02d2e5e5f3c35ce1400e3a2fa2266bb52c4/download diffoscope run passed