Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/f/freebayes/freebayes_1.3.5-3_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/freebayes-1.3.5-3535qm05q/freebayes_1.3.5-3_amd64.buildinfo Get source package info: freebayes=1.3.5-3 Source URL: http://snapshot.notset.fr/mr/package/freebayes/1.3.5-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.4-2 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3+b2 bc=1.07.1-3+b1 binutils=2.37-7 binutils-common=2.37-7 binutils-x86-64-linux-gnu=2.37-7 bsdextrautils=2.37.2-3 bsdutils=1:2.37.2-3 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20210119 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.3.0-11 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 fontconfig=2.13.1-4.2 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-2 g++=4:10.2.1-1 g++-10=10.3.0-11 gcc=4:10.2.1-1 gcc-10=10.3.0-11 gcc-10-base=10.3.0-11 gcc-11-base=11.2.0-8 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=11.2.0-8 libatomic1=11.2.0-8 libattr1=1:2.5.1-1 libaudit-common=1:3.0.5-1 libaudit1=1:3.0.5-1 libbamtools-dev=2.5.1+dfsg-9 libbamtools2.5.1=2.5.1+dfsg-9 libbinutils=2.37-7 libblas3=3.10.0-1 libblkid1=2.37.2-3 libbrotli1=1.0.9-2+b2 libbsd0=0.11.3-1 libbwa-dev=0.7.17-6+b1 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 libcairo2=1.16.0-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-8 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-7 libctf0=2.37-7 libcurl3-gnutls=7.74.0-1.3+b1 libcurl4=7.74.0-1.3+b1 libcurl4-gnutls-dev=7.74.0-1.3+b1 libdatrie1=0.2.13-1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.2 libdeflate-dev=1.7-2 libdeflate0=1.7-2 libdisorder-dev=0.0.2+git20130809.8062ee1-3 libdisorder0=0.0.2+git20130809.8062ee1-3 libdpkg-perl=1.20.9 libelf1=0.185-2 libexpat1=2.4.1-2+b1 libfastahack-dev=1.0.0+dfsg-8 libfastahack0=1.0.0+dfsg-8 libffi8=3.4.2-2 libfile-stripnondeterminism-perl=1.12.0-1 libfml-dev=0.1+git20190320.b499514-1+b1 libfml0=0.1+git20190320.b499514-1+b1 libfontconfig1=2.13.1-4.2 libfreetype6=2.10.4+dfsg-1 libfribidi0=1.0.8-2 libgcc-10-dev=10.3.0-11 libgcc-s1=11.2.0-8 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.21-1 libgdbm6=1.21-1 libgfortran5=11.2.0-8 libglib2.0-0=2.70.0-1+b1 libgmp10=2:6.2.1+dfsg-2 libgnutls30=3.7.2-2 libgomp1=11.2.0-8 libgpg-error0=1.42-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-7 libharfbuzz0b=2.7.4-1 libhogweed6=3.7.3-1 libhts-dev=1.13+ds-2 libhts3=1.13+ds-2 libhtscodecs2=1.1.1-3+b1 libice6=2:1.0.10-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.23-1 libitm1=11.2.0-8 libjbig0=2.1-3.1+b2 libjpeg62-turbo=1:2.0.6-4 libjsoncpp-dev=1.9.4-5 libjsoncpp24=1.9.4-5 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 libldap-2.4-2=2.4.59+dfsg-1 liblsan0=11.2.0-8 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmd0=1.0.4-1 libmount1=2.37.2-3 libmpc3=1.2.0-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.2+20210905-1 libncursesw6=6.2+20210905-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-3 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpango-1.0-0=1.48.10+ds1-1 libpangocairo-1.0-0=1.48.10+ds1-1 libpangoft2-1.0-0=1.48.10+ds1-1 libpaper-utils=1.1.28+b1 libpaper1=1.1.28+b1 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.3-1 libpixman-1-0=0.40.0-1 libpng16-16=1.6.37-3 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libpython3-stdlib=3.9.2-3 libpython3.9-minimal=3.9.7-4 libpython3.9-stdlib=3.9.7-4 libquadmath0=11.2.0-8 libreadline8=8.1-2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.2-2 libselinux1=3.1-3 libsensors-config=1:3.6.0-7 libsensors5=1:3.6.0-7 libseqlib-dev=1.2.0+dfsg-6 libseqlib2=1.2.0+dfsg-6 libsigsegv2=2.13-1 libsm6=2:1.2.3-1 libsmartcols1=2.37.2-3 libsmithwaterman-dev=0.0+git20160702.2610e25-11 libsmithwaterman0=0.0+git20160702.2610e25-11 libsqlite3-0=3.36.0-2 libssh2-1=1.10.0-2 libssl1.1=1.1.1l-1 libssw-dev=1.1-13 libssw0=1.1-13 libstdc++-10-dev=10.3.0-11 libstdc++6=11.2.0-8 libsub-override-perl=0.09-2 libsystemd0=247.9-4 libtabixpp-dev=1.1.0-4 libtabixpp0=1.1.0-4 libtasn1-6=4.17.0-2 libtcl8.6=8.6.11+dfsg-1 libthai-data=0.1.28-4.1 libthai0=0.1.28-4.1 libtiff5=4.3.0-2 libtinfo6=6.2+20210905-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtk8.6=8.6.11.1-1 libtool=2.4.6-15 libtsan0=11.2.0-8 libubsan1=11.2.0-8 libuchardet0=0.0.7-1 libudev1=247.9-4 libunistring2=0.9.10-6 libuuid1=2.37.2-3 libvcflib-dev=1.0.2+dfsg-2 libvcflib-tools=1.0.2+dfsg-2 libvcflib1=1.0.2+dfsg-2 libwebp6=0.6.1-2.1 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libxau6=1:1.0.9-1 libxcb-render0=1.14-3 libxcb-shm0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxft2=2.3.2-2 libxml2=2.9.12+dfsg-5 libxrender1=1:0.9.10-1 libxss1=1:1.2.3-1 libxt6=1:1.2.0-1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.9-2 littler=0.3.14-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 meson=0.59.2-1 ncurses-base=6.2+20210905-1 ncurses-bin=6.2+20210905-1 ninja-build=1.10.1-1 openssl=1.1.1l-1 parallel=20210822+ds-2 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-5 python3=3.9.2-3 python3-distutils=3.9.7-1 python3-lib2to3=3.9.7-1 python3-minimal=3.9.2-3 python3-pkg-resources=52.0.0-4 python3.9=3.9.7-4 python3.9-minimal=3.9.7-4 r-base-core=4.1.1-2 r-cran-cli=3.0.1-1 r-cran-colorspace=2.0-2+dfsg-1 r-cran-crayon=1.4.1-1 r-cran-digest=0.6.28-1 r-cran-ellipsis=0.3.2-2 r-cran-fansi=0.5.0-1 r-cran-farver=2.1.0-1 r-cran-ggplot2=3.3.5+dfsg-2 r-cran-glue=1.4.2-1 r-cran-gridbase=0.4-7-5 r-cran-gtable=0.3.0+dfsg-2 r-cran-isoband=0.2.5-1 r-cran-labeling=0.4.2-1 r-cran-lattice=0.20-45-1 r-cran-lifecycle=1.0.0-1 r-cran-littler=0.3.14-1 r-cran-magrittr=2.0.1-1 r-cran-mass=7.3-54-2 r-cran-matrix=1.3-4-2 r-cran-mgcv=1.8-37-1 r-cran-munsell=0.5.0-2 r-cran-nlme=3.1.153-1 r-cran-pillar=1.6.3+dfsg-1 r-cran-pkgconfig=2.0.3-2 r-cran-pkgkitten=0.2.2-2 r-cran-plyr=1.8.6-2 r-cran-r6=2.5.1-1 r-cran-rcolorbrewer=1.1-2-3 r-cran-rcpp=1.0.7-2 r-cran-rlang=0.4.11-1 r-cran-scales=1.1.1-1 r-cran-tibble=3.1.4+dfsg-2 r-cran-utf8=1.2.2-1 r-cran-vctrs=0.3.8-1 r-cran-viridislite=0.4.0-2 r-cran-withr=2.4.2-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 samtools=1.13-2 sed=4.8-1 sensible-utils=0.0.17 sysstat=12.5.2-2 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 tzdata=2021c-1 ucf=3.0043 unzip=6.0-26 util-linux=2.37.2-3 x11-common=1:7.7+23 xdg-utils=1.1.3-4.1 xz-utils=5.2.5-2 zip=3.0-12 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/20211009T024746Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211009T024746Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211007T204219Z/ 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 freebayes=1.3.5-3 && mkdir -p /build/freebayes-8wZXjy && dpkg-source --no-check -x /*.dsc /build/freebayes-8wZXjy/freebayes-1.3.5 && chown -R builduser:builduser /build/freebayes-8wZXjy" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/freebayes-8wZXjy/freebayes-1.3.5 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1633586967" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/freebayes-8wZXjy /tmp/freebayes-1.3.5-3535qm05q bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211007T204219Z 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.1hC5XmA2O8 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.1hC5XmA2O8 Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-3). 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/20211007T204219Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211007T204219Z 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 (677 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 ... 4667 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/20211009T024746Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211009T024746Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211007T204219Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.1hC5XmA2O8 Get:1 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm InRelease [128 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211007T204219Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main Sources [11.7 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.0 MB in 1min 17s (298 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.1hC5XmA2O8 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d freebayes=1.3.5-3 && mkdir -p /build/freebayes-8wZXjy && dpkg-source --no-check -x /*.dsc /build/freebayes-8wZXjy/freebayes-1.3.5 && chown -R builduser:builduser /build/freebayes-8wZXjy"' exec /tmp/mmdebstrap.1hC5XmA2O8 Reading package lists... NOTICE: 'freebayes' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/freebayes.git Please use: git clone https://salsa.debian.org/med-team/freebayes.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2904 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main freebayes 1.3.5-3 (dsc) [2221 B] Get:2 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main freebayes 1.3.5-3 (tar) [2890 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211009T024746Z bookworm/main freebayes 1.3.5-3 (diff) [11.4 kB] Fetched 2904 kB in 3s (988 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'freebayes_1.3.5-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting freebayes in /build/freebayes-8wZXjy/freebayes-1.3.5 dpkg-source: info: unpacking freebayes_1.3.5.orig.tar.gz dpkg-source: info: unpacking freebayes_1.3.5-3.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/freebayes-8wZXjy/freebayes-1.3.5 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1633586967" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.1hC5XmA2O8 dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.5-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=meson --builddir=build dh_auto_clean -O--buildsystem=meson -O--builddir=build dh_autoreconf_clean -O--buildsystem=meson -O--builddir=build dh_clean -O--buildsystem=meson -O--builddir=build debian/rules binary-arch dh binary-arch --buildsystem=meson --builddir=build dh_update_autotools_config -a -O--buildsystem=meson -O--builddir=build dh_autoreconf -a -O--buildsystem=meson -O--builddir=build dh_auto_configure -a -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu The Meson build system Version: 0.59.2 Source dir: /build/freebayes-8wZXjy/freebayes-1.3.5 Build dir: /build/freebayes-8wZXjy/freebayes-1.3.5/build Build type: native build Project name: freebayes Project version: 1.3.4 C compiler for the host machine: cc (gcc 10.3.0 "cc (Debian 10.3.0-11) 10.3.0") C linker for the host machine: cc ld.bfd 2.37 C++ compiler for the host machine: c++ (gcc 10.3.0 "c++ (Debian 10.3.0-11) 10.3.0") C++ linker for the host machine: c++ ld.bfd 2.37 Host machine cpu family: x86_64 Host machine cpu: x86_64 Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency zlib found: YES 1.2.11 Run-time dependency liblzma found: YES 5.2.5 Run-time dependency threads found: YES Run-time dependency htslib found: YES 1.13+ds Library tabixpp found: YES Run-time dependency libvcflib found: YES 1.0 Run-time dependency libseqlib found: YES 1.0 Compiler for C++ supports arguments -fpermissive: YES Compiler for C++ supports arguments -Wno-reorder: YES Compiler for C++ supports arguments -Wno-sign-compare: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Program prove found: YES (/usr/bin/prove) Build targets in project: 3 Option optimization is: 0 [default: 3] Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build -a -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 ninja -j10 -v [1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp [2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp [3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp [4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp [5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp [6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp [7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp [8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp [9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp [10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp [11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp [12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp [13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp [14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp [15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp [16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp [17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp [18/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp [19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp ../src/Allele.cpp: In member function ‘const short int Allele::currentQuality() const’: ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not handled in switch [-Wswitch] 160 | switch (this->type) { | ^ ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not handled in switch [-Wswitch] [20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmathuint.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<1>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ In file included from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmathint.h:652:40: warning: ‘result.ttmath::UInt<4>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmathint.h:652:40: warning: ‘result.ttmath::UInt<4>::table[3]’ may be used uninitialized in this function [-Wmaybe-uninitialized] ../ttmath/ttmathint.h:652:40: warning: ‘result.ttmath::UInt<4>::table[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] ../ttmath/ttmathint.h:652:40: warning: ‘result.ttmath::UInt<4>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<1>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ In file included from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmathint.h:652:40: warning: ‘result.ttmath::UInt<4>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmathint.h:652:40: warning: ‘result.ttmath::UInt<4>::table[3]’ may be used uninitialized in this function [-Wmaybe-uninitialized] ../ttmath/ttmathint.h:652:40: warning: ‘result.ttmath::UInt<4>::table[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] ../ttmath/ttmathint.h:652:40: warning: ‘result.ttmath::UInt<4>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] [21/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp [22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp [23/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp [24/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp [25/27] rm -f libfreebayes_common.a && gcc-ar csrD libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o [26/27] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so -pthread /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/libvcflib.so /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/libdisorder.so /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/libfastahack.so /usr/lib/x86_64-linux-gnu/libseqlib.so /usr/lib/libbwa.a -ltabixpp -Wl,--end-group [27/27] c++ -o freebayes freebayes.p/src_freebayes.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/freebayes-8wZXjy/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so -pthread /usr/lib/x86_64-linux-gnu/libhts.so -ltabixpp /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/libvcflib.so /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/libdisorder.so /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/libfastahack.so /usr/lib/x86_64-linux-gnu/libseqlib.so /usr/lib/libbwa.a -ltabixpp -Wl,--end-group create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=meson -O--builddir=build dh_prep -a -O--buildsystem=meson -O--builddir=build dh_auto_install --destdir=debian/freebayes/ -a -O--buildsystem=meson -O--builddir=build cd build && DESTDIR=/build/freebayes-8wZXjy/freebayes-1.3.5/debian/freebayes LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing freebayes to /build/freebayes-8wZXjy/freebayes-1.3.5/debian/freebayes/usr/bin Installing bamleftalign to /build/freebayes-8wZXjy/freebayes-1.3.5/debian/freebayes/usr/bin dh_installdocs -a -O--buildsystem=meson -O--builddir=build dh_installchangelogs -a -O--buildsystem=meson -O--builddir=build dh_installexamples -a -O--buildsystem=meson -O--builddir=build dh_installsystemduser -a -O--buildsystem=meson -O--builddir=build dh_perl -a -O--buildsystem=meson -O--builddir=build dh_link -a -O--buildsystem=meson -O--builddir=build dh_strip_nondeterminism -a -O--buildsystem=meson -O--builddir=build dh_compress -a -O--buildsystem=meson -O--builddir=build dh_fixperms -a -O--buildsystem=meson -O--builddir=build dh_missing -a -O--buildsystem=meson -O--builddir=build dh_dwz -a -O--buildsystem=meson -O--builddir=build dh_strip -a -O--buildsystem=meson -O--builddir=build dh_makeshlibs -a -O--buildsystem=meson -O--builddir=build dh_shlibdeps -a -O--buildsystem=meson -O--builddir=build dh_installdeb -a -O--buildsystem=meson -O--builddir=build dh_gencontrol -a -O--buildsystem=meson -O--builddir=build dh_md5sums -a -O--buildsystem=meson -O--builddir=build dh_builddeb -a -O--buildsystem=meson -O--builddir=build dpkg-deb: building package 'freebayes' in '../freebayes_1.3.5-3_amd64.deb'. dpkg-deb: building package 'freebayes-dbgsym' in '../freebayes-dbgsym_1.3.5-3_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../freebayes_1.3.5-3_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/freebayes-8wZXjy /tmp/freebayes-1.3.5-3535qm05q I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.1hC5XmA2O8... I: success in 3087.9153 seconds md5: freebayes-dbgsym_1.3.5-3_amd64.deb: OK md5: Value of 'md5' differs for freebayes_1.3.5-3_amd64.deb md5: Size differs for freebayes_1.3.5-3_amd64.deb sha1: freebayes-dbgsym_1.3.5-3_amd64.deb: OK sha1: Value of 'sha1' differs for freebayes_1.3.5-3_amd64.deb sha1: Size differs for freebayes_1.3.5-3_amd64.deb sha256: freebayes-dbgsym_1.3.5-3_amd64.deb: OK sha256: Value of 'sha256' differs for freebayes_1.3.5-3_amd64.deb sha256: Size differs for freebayes_1.3.5-3_amd64.deb Checksums: FAIL diffoscope run passed