DC-Build-Header: freebayes 1.3.2-3 / 2020-10-29 19:46:07 +0000 DC-Task: type:rebuild-binarch-only source:freebayes version:1.3.2-3 chroot:unstable esttime:128 logfile:/tmp/freebayes_1.3.2-3_unstable_clang11.log modes:clang11:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang11 freebayes_1.3.2-3' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-9-59.eu-central-1.compute.internal +==============================================================================+ | freebayes 1.3.2-3 (amd64) Thu, 29 Oct 2020 19:46:07 +0000 | +==============================================================================+ Package: freebayes Version: 1.3.2-3 Source Version: 1.3.2-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-85fc8328-69bd-4f0a-a976-a316ec96ae47' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang11 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=10 + echo 'Install of clang-10' Install of clang-10 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [146 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [734 B] Ign:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [734 B] Ign:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index Get:4 http://127.0.0.1:12990/debian sid/main Translation-en [6391 kB] Get:5 http://127.0.0.1:12990/debian sid/main Sources [8989 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 Packages [8492 kB] Fetched 24.0 MB in 3s (6981 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-10 libomp-10-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1 libgcc-9-dev libllvm10 libobjc-10-dev libobjc4 libomp5-10 libz3-4 Suggested packages: clang-10-doc libomp-10-doc Recommended packages: llvm-10-dev python3 The following NEW packages will be installed: clang-10 lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1 libgcc-9-dev libllvm10 libobjc-10-dev libobjc-9-dev libobjc4 libomp-10-dev libomp5-10 libz3-4 0 upgraded, 19 newly installed, 0 to remove and 1 not upgraded. Need to get 52.3 MB of archives. After this operation, 274 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.9-1 [6783 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libllvm10 amd64 1:10.0.1-7 [16.6 MB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp10 amd64 1:10.0.1-7 [9069 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libgc1 amd64 1:8.0.4-2.1 [239 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10.2.0-15 [41.6 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libobjc-10-dev amd64 10.2.0-15 [170 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.31-4 [2815 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10.2.0-15 [49.4 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10.2.0-15 [511 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-10-dev amd64 1:10.0.1-7 [5062 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libclang1-10 amd64 1:10.0.1-7 [7293 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 clang-10 amd64 1:10.0.1-7 [106 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.3.0-18 [390 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.3.0-18 [2347 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.3.0-18 [220 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libomp5-10 amd64 1:10.0.1-7 [339 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libomp-10-dev amd64 1:10.0.1-7 [86.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 52.3 MB in 0s (136 MB/s) Selecting previously unselected package libbsd0: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 ... 12312 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../01-libedit2_3.1-20191231-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20191231-1) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../02-libz3-4_4.8.9-1_amd64.deb ... Unpacking libz3-4:amd64 (4.8.9-1) ... Selecting previously unselected package libllvm10:amd64. Preparing to unpack .../03-libllvm10_1%3a10.0.1-7_amd64.deb ... Unpacking libllvm10:amd64 (1:10.0.1-7) ... Selecting previously unselected package libclang-cpp10. Preparing to unpack .../04-libclang-cpp10_1%3a10.0.1-7_amd64.deb ... Unpacking libclang-cpp10 (1:10.0.1-7) ... Selecting previously unselected package libgc1:amd64. Preparing to unpack .../05-libgc1_1%3a8.0.4-2.1_amd64.deb ... Unpacking libgc1:amd64 (1:8.0.4-2.1) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../06-libobjc4_10.2.0-15_amd64.deb ... Unpacking libobjc4:amd64 (10.2.0-15) ... Selecting previously unselected package libobjc-10-dev:amd64. Preparing to unpack .../07-libobjc-10-dev_10.2.0-15_amd64.deb ... Unpacking libobjc-10-dev:amd64 (10.2.0-15) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../08-libc6-i386_2.31-4_amd64.deb ... 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Unpacking libasan5:amd64 (9.3.0-18) ... Selecting previously unselected package libgcc-9-dev:amd64. Preparing to unpack .../15-libgcc-9-dev_9.3.0-18_amd64.deb ... Unpacking libgcc-9-dev:amd64 (9.3.0-18) ... Selecting previously unselected package libobjc-9-dev:amd64. Preparing to unpack .../16-libobjc-9-dev_9.3.0-18_amd64.deb ... Unpacking libobjc-9-dev:amd64 (9.3.0-18) ... Selecting previously unselected package libomp5-10:amd64. Preparing to unpack .../17-libomp5-10_1%3a10.0.1-7_amd64.deb ... Unpacking libomp5-10:amd64 (1:10.0.1-7) ... Selecting previously unselected package libomp-10-dev. Preparing to unpack .../18-libomp-10-dev_1%3a10.0.1-7_amd64.deb ... Unpacking libomp-10-dev (1:10.0.1-7) ... Setting up libasan5:amd64 (9.3.0-18) ... Setting up libz3-4:amd64 (4.8.9-1) ... Setting up libgc1:amd64 (1:8.0.4-2.1) ... Setting up libomp5-10:amd64 (1:10.0.1-7) ... Setting up libc6-i386 (2.31-4) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libomp-10-dev (1:10.0.1-7) ... Setting up libedit2:amd64 (3.1-20191231-1) ... Setting up libobjc4:amd64 (10.2.0-15) ... Setting up libllvm10:amd64 (1:10.0.1-7) ... Setting up libgcc-9-dev:amd64 (9.3.0-18) ... Setting up lib32gcc-s1 (10.2.0-15) ... Setting up lib32stdc++6 (10.2.0-15) ... Setting up libclang1-10 (1:10.0.1-7) ... Setting up libobjc-9-dev:amd64 (9.3.0-18) ... Setting up libobjc-10-dev:amd64 (10.2.0-15) ... Setting up libclang-common-10-dev (1:10.0.1-7) ... Setting up libclang-cpp10 (1:10.0.1-7) ... Setting up clang-10 (1:10.0.1-7) ... Processing triggers for libc-bin (2.31-4) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8 9 10' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-10 g++-4.6 + ln -s clang-10 gcc-4.6 + ln -s clang-10 cpp-4.6 + ln -s clang-10 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-10 g++-4.7 + ln -s clang-10 gcc-4.7 + ln -s clang-10 cpp-4.7 + ln -s clang-10 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-10 g++-4.8 + ln -s clang-10 gcc-4.8 + ln -s clang-10 cpp-4.8 + ln -s clang-10 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-10 g++-4.9 + ln -s clang-10 gcc-4.9 + ln -s clang-10 cpp-4.9 + ln -s clang-10 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-10 g++-5 + ln -s clang-10 gcc-5 + ln -s clang-10 cpp-5 + ln -s clang-10 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-10 g++-6 + ln -s clang-10 gcc-6 + ln -s clang-10 cpp-6 + ln -s clang-10 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-10 g++-7 + ln -s clang-10 gcc-7 + ln -s clang-10 cpp-7 + ln -s clang-10 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-10 g++-8 + ln -s clang-10 gcc-8 + ln -s clang-10 cpp-8 + ln -s clang-10 gcc + echo 'gcc-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-9 gcc-9 cpp-9 gcc + ln -s clang++-10 g++-9 + ln -s clang-10 gcc-9 + ln -s clang-10 cpp-9 + ln -s clang-10 gcc + echo 'gcc-9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-10 gcc-10 cpp-10 gcc + ln -s clang++-10 g++-10 + ln -s clang-10 gcc-10 + ln -s clang-10 cpp-10 + ln -s clang-10 gcc + echo 'gcc-10 hold' + dpkg --set-selections + echo 'g++-10 hold' + dpkg --set-selections + cd - /build/freebayes-MobRM9 + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang + cd /usr/bin/ + rm -f clang++ clang + ln -s clang-10 clang++ + ln -s clang-10 clang + clang++ --version Debian clang version 10.0.1-7 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + clang --version Debian clang version 10.0.1-7 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + cd - /build/freebayes-MobRM9 + apt install --yes --no-install-recommends --force-yes qt5-qmake WARNING: apt does not have a stable CLI interface. Use with caution in scripts. Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: qt5-qmake-bin qtchooser The following NEW packages will be installed: qt5-qmake qt5-qmake-bin qtchooser 0 upgraded, 3 newly installed, 0 to remove and 1 not upgraded. Need to get 1304 kB of archives. After this operation, 4865 kB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.14.2+dfsg-6 [1035 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 qtchooser amd64 66-2 [26.3 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake amd64 5.14.2+dfsg-6 [242 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1304 kB in 0s (21.2 MB/s) Selecting previously unselected package qt5-qmake-bin. (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 ... 13315 files and directories currently installed.) Preparing to unpack .../qt5-qmake-bin_5.14.2+dfsg-6_amd64.deb ... Unpacking qt5-qmake-bin (5.14.2+dfsg-6) ... Selecting previously unselected package qtchooser. Preparing to unpack .../qtchooser_66-2_amd64.deb ... Unpacking qtchooser (66-2) ... Selecting previously unselected package qt5-qmake:amd64. Preparing to unpack .../qt5-qmake_5.14.2+dfsg-6_amd64.deb ... Unpacking qt5-qmake:amd64 (5.14.2+dfsg-6) ... Setting up qt5-qmake-bin (5.14.2+dfsg-6) ... Setting up qtchooser (66-2) ... Setting up qt5-qmake:amd64 (5.14.2+dfsg-6) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + cp /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qmake.conf /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qplatformdefs.h /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ + ls -al /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ total 16 drwxr-xr-x 2 root root 4096 Oct 29 19:46 . drwxr-xr-x 76 root root 4096 Oct 29 19:46 .. -rw-r--r-- 1 root root 276 Oct 29 19:46 qmake.conf -rw-r--r-- 1 root root 3218 Oct 29 19:46 qplatformdefs.h + cat /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/qmake.conf # # qmake configuration for linux-clang # MAKEFILE_GENERATOR = UNIX CONFIG += incremental QMAKE_INCREMENTAL_STYLE = sublib include(../common/linux.conf) include(../common/gcc-base-unix.conf) include(../common/clang.conf) QMAKE_LFLAGS += -ccc-gcc-name g++ load(qt_config) + export QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + sed -i -e 's|compare_problem(2,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + sed -i -e 's|compare_problem(1,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + grep 'compare_problem(' /usr/bin/dpkg-gensymbols compare_problem(4, g_('new libraries appeared in the symbols file: %s'), "@libs"); compare_problem(3, g_('some libraries disappeared in the symbols file: %s'), "@libs"); compare_problem(0, g_('some new symbols appeared in the symbols file: %s'), compare_problem(0, g_('some symbols or patterns disappeared in the symbols file: %s'), I: Finished running '/tmp/clang11'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/freebayes-MobRM9/resolver-IklpEC' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:12990/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libdebconfclient0 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 49.6 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libdebconfclient0 amd64 0.255 [49.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 49.6 kB in 0s (3511 kB/s) (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 ... 14056 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.255_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.255) over (0.254) ... Setting up libdebconfclient0:amd64 (0.255) ... Processing triggers for libc-bin (2.31-4) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ 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 2661 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main freebayes 1.3.2-3 (dsc) [2240 B] Get:2 http://127.0.0.1:12990/debian sid/main freebayes 1.3.2-3 (tar) [2642 kB] Get:3 http://127.0.0.1:12990/debian sid/main freebayes 1.3.2-3 (diff) [16.5 kB] Fetched 2661 kB in 0s (22.6 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/freebayes-MobRM9/freebayes-1.3.2' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-MobRM9' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, pkg-config, python3, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), cmake, pkg-config, python3, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6), build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [484 B] Get:5 copy:/<>/apt_archive ./ Packages [556 B] Fetched 1997 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bsdextrautils ca-certificates cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbwa-dev libcairo2 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libice6 libicu67 libjbig0 libjpeg62-turbo libjsoncpp-dev libjsoncpp1 liblapack3 libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libncurses6 libncursesw6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libreadline8 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib1 libsigsegv2 libsm6 libsmithwaterman-dev libsmithwaterman0 libsqlite3-0 libssh2-1 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler m4 man-db mime-support openssl parallel pkg-config po-debconf procps python3 python3-minimal python3.8 python3.8-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr readline-common samtools sensible-utils sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libbamtools-doc libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc lm-sensors tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown r-cran-prettycode r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-stringr r-cran-magick r-cran-getopt r-cran-bit64 r-cran-bitops r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-curl r-cran-inline r-cran-mockr r-cran-dichromat r-cran-devtools r-cran-usethis r-cran-blob r-cran-formattable r-cran-hms r-cran-htmltools r-cran-purrr r-cran-tidyr r-cran-zeallot readline-doc cwltool isag Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common libgpm2 publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl psmisc r-recommended r-base-dev r-doc-html r-cran-cliapp r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-quantreg r-cran-lubridate r-cran-domc r-cran-abind r-cran-codetools r-cran-curl r-cran-rmarkdown r-cran-bit64 r-cran-hms r-cran-xml2 r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-mockr r-cran-generics r-cran-waldo r-cran-dbi systemd | cron | cron-daemon libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bsdextrautils ca-certificates cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbwa-dev libcairo2 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libice6 libicu67 libjbig0 libjpeg62-turbo libjsoncpp-dev libjsoncpp1 liblapack3 libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libncurses6 libncursesw6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libreadline8 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib1 libsigsegv2 libsm6 libsmithwaterman-dev libsmithwaterman0 libsqlite3-0 libssh2-1 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler m4 man-db mime-support openssl parallel pkg-config po-debconf procps python3 python3-minimal python3.8 python3.8-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr readline-common samtools sbuild-build-depends-main-dummy sensible-utils sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 202 newly installed, 0 to remove and 0 not upgraded. Need to get 118 MB of archives. After this operation, 297 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [980 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdextrautils amd64 2.36-3+b1 [140 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.3-2 [1314 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-minimal amd64 3.8.6-1 [761 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.2.10-1 [96.9 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 python3.8-minimal amd64 3.8.6-1 [1863 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 python3-minimal amd64 3.8.6-1 [37.7 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 mime-support all 3.64 [37.8 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libncursesw6 amd64 6.2+20200918-1 [132 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 readline-common all 8.0-4 [72.5 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.33.0-1 [790 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-stdlib amd64 3.8.6-1 [1720 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 python3.8 amd64 3.8.6-1 [422 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libpython3-stdlib amd64 3.8.6-1 [20.9 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 python3 amd64 3.8.6-1 [64.0 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libncurses6 amd64 6.2+20200918-1 [102 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 libprocps8 amd64 2:3.3.16-5 [62.7 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 procps amd64 2:3.3.16-5 [262 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-5 [120 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-5 [67.9 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 ucf all 3.0043 [74.0 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:31 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.69-11.1 [341 kB] Get:32 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:33 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.2-4 [801 kB] Get:34 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:35 http://127.0.0.1:12990/debian sid/main amd64 bc amd64 1.07.1-2+b2 [109 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 openssl amd64 1.1.1h-1 [848 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 ca-certificates all 20200601 [158 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 cmake-data all 3.18.4-1 [1725 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 libicu67 amd64 67.1-4 [8624 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.10+dfsg-6.1 [692 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 libarchive13 amd64 3.4.3-2 [342 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 libbrotli1 amd64 1.0.9-2+b1 [282 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [69.0 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [106 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libldap-2.4-2 amd64 2.4.54+dfsg-1 [231 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 libnghttp2-14 amd64 1.41.0-3 [74.0 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 libpsl5 amd64 0.21.0-1.1 [55.3 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:49 http://127.0.0.1:12990/debian sid/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 libcurl4 amd64 7.72.0-1 [336 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 libjsoncpp1 amd64 1.7.4-3.1 [77.6 kB] Get:52 http://127.0.0.1:12990/debian sid/main amd64 librhash0 amd64 1.4.0-1 [124 kB] Get:53 http://127.0.0.1:12990/debian sid/main amd64 libuv1 amd64 1.39.0-1 [131 kB] Get:54 http://127.0.0.1:12990/debian sid/main amd64 cmake amd64 3.18.4-1 [5599 kB] Get:55 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-14 [513 kB] Get:56 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:57 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13.2.1 [188 kB] Get:58 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:59 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:60 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB] Get:61 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.9.0-1 [15.2 kB] Get:62 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.181-1 [164 kB] Get:63 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.13-5 [151 kB] Get:64 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.66.1-2 [1362 kB] Get:65 http://127.0.0.1:12990/debian sid/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:66 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:67 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:68 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:69 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13.2.1 [1007 kB] Get:70 http://127.0.0.1:12990/debian sid/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:71 http://127.0.0.1:12990/debian sid/main amd64 libfreetype6 amd64 2.10.2+dfsg-4 [410 kB] Get:72 http://127.0.0.1:12990/debian sid/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:73 http://127.0.0.1:12990/debian sid/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:74 http://127.0.0.1:12990/debian sid/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:75 http://127.0.0.1:12990/debian sid/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get:76 http://127.0.0.1:12990/debian sid/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-7 [161 kB] Get:77 http://127.0.0.1:12990/debian sid/main amd64 libbamtools-dev amd64 2.5.1+dfsg-7 [212 kB] Get:78 http://127.0.0.1:12990/debian sid/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get:79 http://127.0.0.1:12990/debian sid/main amd64 libbwa-dev amd64 0.7.17-5 [146 kB] Get:80 http://127.0.0.1:12990/debian sid/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:81 http://127.0.0.1:12990/debian sid/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:82 http://127.0.0.1:12990/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:83 http://127.0.0.1:12990/debian sid/main amd64 libxcb1 amd64 1.14-2 [139 kB] Get:84 http://127.0.0.1:12990/debian sid/main amd64 libx11-data all 2:1.6.12-1 [311 kB] Get:85 http://127.0.0.1:12990/debian sid/main amd64 libx11-6 amd64 2:1.6.12-1 [770 kB] Get:86 http://127.0.0.1:12990/debian sid/main amd64 libxcb-render0 amd64 1.14-2 [111 kB] Get:87 http://127.0.0.1:12990/debian sid/main amd64 libxcb-shm0 amd64 1.14-2 [101 kB] Get:88 http://127.0.0.1:12990/debian sid/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:89 http://127.0.0.1:12990/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:90 http://127.0.0.1:12990/debian sid/main amd64 libcairo2 amd64 1.16.0-4 [689 kB] Get:91 http://127.0.0.1:12990/debian sid/main amd64 libcurl3-gnutls amd64 7.72.0-1 [333 kB] Get:92 http://127.0.0.1:12990/debian sid/main amd64 libcurl4-gnutls-dev amd64 7.72.0-1 [422 kB] Get:93 http://127.0.0.1:12990/debian sid/main amd64 libdatrie1 amd64 0.2.12-3 [39.5 kB] Get:94 http://127.0.0.1:12990/debian sid/main amd64 libdeflate0 amd64 1.6-1 [55.1 kB] Get:95 http://127.0.0.1:12990/debian sid/main amd64 libdeflate-dev amd64 1.6-1 [46.5 kB] Get:96 http://127.0.0.1:12990/debian sid/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-1 [4264 B] Get:97 http://127.0.0.1:12990/debian sid/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-1 [4212 B] Get:98 http://127.0.0.1:12990/debian sid/main amd64 libfastahack0 amd64 1.0.0+dfsg-6 [25.5 kB] Get:99 http://127.0.0.1:12990/debian sid/main amd64 libfastahack-dev amd64 1.0.0+dfsg-6 [26.9 kB] Get:100 http://127.0.0.1:12990/debian sid/main amd64 libfml0 amd64 0.1-13 [70.8 kB] Get:101 http://127.0.0.1:12990/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:102 http://127.0.0.1:12990/debian sid/main amd64 libfml-dev amd64 0.1-13 [82.1 kB] Get:103 http://127.0.0.1:12990/debian sid/main amd64 libfribidi0 amd64 1.0.8-2 [64.8 kB] Get:104 http://127.0.0.1:12990/debian sid/main amd64 libgfortran5 amd64 10.2.0-15 [728 kB] Get:105 http://127.0.0.1:12990/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:106 http://127.0.0.1:12990/debian sid/main amd64 libharfbuzz0b amd64 2.6.7-1 [1467 kB] Get:107 http://127.0.0.1:12990/debian sid/main amd64 libhts3 amd64 1.11-2 [373 kB] Get:108 http://127.0.0.1:12990/debian sid/main amd64 liblzma-dev amd64 5.2.4-1+b1 [211 kB] Get:109 http://127.0.0.1:12990/debian sid/main amd64 libhts-dev amd64 1.11-2 [3859 kB] Get:110 http://127.0.0.1:12990/debian sid/main amd64 x11-common all 1:7.7+21 [252 kB] Get:111 http://127.0.0.1:12990/debian sid/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:112 http://127.0.0.1:12990/debian sid/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:113 http://127.0.0.1:12990/debian sid/main amd64 libjpeg62-turbo amd64 1:2.0.5-1.1 [149 kB] Get:114 http://127.0.0.1:12990/debian sid/main amd64 libjsoncpp-dev amd64 1.7.4-3.1 [93.0 kB] Get:115 http://127.0.0.1:12990/debian sid/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get:116 http://127.0.0.1:12990/debian sid/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:117 http://127.0.0.1:12990/debian sid/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:118 http://127.0.0.1:12990/debian sid/main amd64 libpango-1.0-0 amd64 1.46.2-1 [191 kB] Get:119 http://127.0.0.1:12990/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.46.2-1 [61.2 kB] Get:120 http://127.0.0.1:12990/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.46.2-1 [50.0 kB] Get:121 http://127.0.0.1:12990/debian sid/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:122 http://127.0.0.1:12990/debian sid/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:123 http://127.0.0.1:12990/debian sid/main amd64 libsensors-config all 1:3.6.0-2 [32.0 kB] Get:124 http://127.0.0.1:12990/debian sid/main amd64 libsensors5 amd64 1:3.6.0-2 [53.1 kB] Get:125 http://127.0.0.1:12990/debian sid/main amd64 libssw0 amd64 1.1-11+b1 [19.8 kB] Get:126 http://127.0.0.1:12990/debian sid/main amd64 libseqlib1 amd64 1.1.2+dfsg-9 [119 kB] Get:127 http://127.0.0.1:12990/debian sid/main amd64 libssw-dev amd64 1.1-11+b1 [22.5 kB] Get:128 http://127.0.0.1:12990/debian sid/main amd64 libseqlib-dev amd64 1.1.2+dfsg-9 [167 kB] Get:129 http://127.0.0.1:12990/debian sid/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:130 http://127.0.0.1:12990/debian sid/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-9 [36.0 kB] Get:131 http://127.0.0.1:12990/debian sid/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-9 [39.0 kB] Get:132 http://127.0.0.1:12990/debian sid/main amd64 libtabixpp0 amd64 1.1.0-3 [8712 B] Get:133 http://127.0.0.1:12990/debian sid/main amd64 libtabixpp-dev amd64 1.1.0-3 [7824 B] Get:134 http://127.0.0.1:12990/debian sid/main amd64 libtcl8.6 amd64 8.6.10+dfsg-1 [1007 kB] Get:135 http://127.0.0.1:12990/debian sid/main amd64 libwebp6 amd64 0.6.1-2+b1 [261 kB] Get:136 http://127.0.0.1:12990/debian sid/main amd64 libtiff5 amd64 4.1.0+git191117-2 [271 kB] Get:137 http://127.0.0.1:12990/debian sid/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:138 http://127.0.0.1:12990/debian sid/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:139 http://127.0.0.1:12990/debian sid/main amd64 libtk8.6 amd64 8.6.10-1 [773 kB] Get:140 http://127.0.0.1:12990/debian sid/main amd64 libvcflib1 amd64 1.0.1+dfsg-3 [152 kB] Get:141 http://127.0.0.1:12990/debian sid/main amd64 libvcflib-dev amd64 1.0.1+dfsg-3 [28.7 kB] Get:142 http://127.0.0.1:12990/debian sid/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:143 http://127.0.0.1:12990/debian sid/main amd64 unzip amd64 6.0-25 [172 kB] Get:144 http://127.0.0.1:12990/debian sid/main amd64 xdg-utils all 1.1.3-2 [74.6 kB] Get:145 http://127.0.0.1:12990/debian sid/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:146 http://127.0.0.1:12990/debian sid/main amd64 r-base-core amd64 4.0.3-1 [25.1 MB] Get:147 http://127.0.0.1:12990/debian sid/main amd64 r-cran-littler amd64 0.3.12-1 [95.9 kB] Get:148 http://127.0.0.1:12990/debian sid/main amd64 littler all 0.3.12-1 [15.6 kB] Get:149 http://127.0.0.1:12990/debian sid/main amd64 r-cran-pkgkitten all 0.2.0-1 [25.3 kB] Get:150 http://127.0.0.1:12990/debian sid/main amd64 r-cran-rcpp amd64 1.0.5-1 [2051 kB] Get:151 http://127.0.0.1:12990/debian sid/main amd64 r-cran-plyr amd64 1.8.6-2 [830 kB] Get:152 http://127.0.0.1:12990/debian sid/main amd64 r-cran-digest amd64 0.6.27-1 [192 kB] Get:153 http://127.0.0.1:12990/debian sid/main amd64 r-cran-glue amd64 1.4.2-1 [138 kB] Get:154 http://127.0.0.1:12990/debian sid/main amd64 r-cran-gtable all 0.3.0+dfsg-2 [163 kB] Get:155 http://127.0.0.1:12990/debian sid/main amd64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get:156 http://127.0.0.1:12990/debian sid/main amd64 r-cran-crayon all 1.3.4-5 [750 kB] Get:157 http://127.0.0.1:12990/debian sid/main amd64 r-cran-fansi amd64 0.4.1-1+b1 [345 kB] Get:158 http://127.0.0.1:12990/debian sid/main amd64 r-cran-cli all 2.1.0-1 [410 kB] Get:159 http://127.0.0.1:12990/debian sid/main amd64 r-cran-rlang amd64 0.4.8-1 [1141 kB] Get:160 http://127.0.0.1:12990/debian sid/main amd64 r-cran-ellipsis amd64 0.3.1-1 [31.7 kB] Get:161 http://127.0.0.1:12990/debian sid/main amd64 r-cran-evaluate all 0.14-2 [81.1 kB] Get:162 http://127.0.0.1:12990/debian sid/main amd64 r-cran-magrittr all 1.5-6 [154 kB] Get:163 http://127.0.0.1:12990/debian sid/main amd64 r-cran-r6 all 2.4.1-2 [79.2 kB] Get:164 http://127.0.0.1:12990/debian sid/main amd64 r-cran-backports amd64 1.1.10-1 [81.0 kB] Get:165 http://127.0.0.1:12990/debian sid/main amd64 r-cran-rprojroot all 1.3-2-3 [97.5 kB] Get:166 http://127.0.0.1:12990/debian sid/main amd64 r-cran-desc all 1.2.0-3 [301 kB] Get:167 http://127.0.0.1:12990/debian sid/main amd64 r-cran-ps amd64 1.4.0-1 [253 kB] Get:168 http://127.0.0.1:12990/debian sid/main amd64 r-cran-processx amd64 3.4.4-1 [295 kB] Get:169 http://127.0.0.1:12990/debian sid/main amd64 r-cran-callr all 3.5.1-1 [386 kB] Get:170 http://127.0.0.1:12990/debian sid/main amd64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get:171 http://127.0.0.1:12990/debian sid/main amd64 r-cran-withr all 2.3.0-1 [209 kB] Get:172 http://127.0.0.1:12990/debian sid/main amd64 r-cran-pkgbuild all 1.1.0-1 [144 kB] Get:173 http://127.0.0.1:12990/debian sid/main amd64 r-cran-rstudioapi all 0.11-2 [249 kB] Get:174 http://127.0.0.1:12990/debian sid/main amd64 r-cran-pkgload amd64 1.1.0-1 [168 kB] Get:175 http://127.0.0.1:12990/debian sid/main amd64 r-cran-praise all 1.0.0-4 [20.1 kB] Get:176 http://127.0.0.1:12990/debian sid/main amd64 r-cran-testthat amd64 2.3.2-2+b1 [1069 kB] Get:177 http://127.0.0.1:12990/debian sid/main amd64 r-cran-isoband amd64 0.2.2-1 [2468 kB] Get:178 http://127.0.0.1:12990/debian sid/main amd64 r-cran-mass amd64 7.3-53-1 [1112 kB] Get:179 http://127.0.0.1:12990/debian sid/main amd64 r-cran-lattice amd64 0.20-41-1+b1 [1164 kB] Get:180 http://127.0.0.1:12990/debian sid/main amd64 r-cran-nlme amd64 3.1.150-1 [2218 kB] Get:181 http://127.0.0.1:12990/debian sid/main amd64 r-cran-matrix amd64 1.2-18-1+b1 [3487 kB] Get:182 http://127.0.0.1:12990/debian sid/main amd64 r-cran-mgcv amd64 1.8-33-1 [2987 kB] Get:183 http://127.0.0.1:12990/debian sid/main amd64 r-cran-farver amd64 2.0.3-1+b1 [1393 kB] Get:184 http://127.0.0.1:12990/debian sid/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get:185 http://127.0.0.1:12990/debian sid/main amd64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get:186 http://127.0.0.1:12990/debian sid/main amd64 r-cran-colorspace amd64 1.4-1+dfsg-2 [1640 kB] Get:187 http://127.0.0.1:12990/debian sid/main amd64 r-cran-munsell all 0.5.0-2 [236 kB] Get:188 http://127.0.0.1:12990/debian sid/main amd64 r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB] Get:189 http://127.0.0.1:12990/debian sid/main amd64 r-cran-viridislite all 0.3.0-4 [59.2 kB] Get:190 http://127.0.0.1:12990/debian sid/main amd64 r-cran-scales all 1.1.1-1 [557 kB] Get:191 http://127.0.0.1:12990/debian sid/main amd64 r-cran-utf8 amd64 1.1.4-2 [131 kB] Get:192 http://127.0.0.1:12990/debian sid/main amd64 r-cran-vctrs amd64 0.3.4-1 [1076 kB] Get:193 http://127.0.0.1:12990/debian sid/main amd64 r-cran-pillar all 1.4.6-1 [227 kB] Get:194 http://127.0.0.1:12990/debian sid/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get:195 http://127.0.0.1:12990/debian sid/main amd64 r-cran-tibble amd64 3.0.4-1 [427 kB] Get:196 http://127.0.0.1:12990/debian sid/main amd64 r-cran-ggplot2 all 3.3.2+dfsg-2 [3146 kB] Get:197 http://127.0.0.1:12990/debian sid/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB] Get:198 http://127.0.0.1:12990/debian sid/main amd64 libvcflib-tools amd64 1.0.1+dfsg-3 [637 kB] Get:199 http://127.0.0.1:12990/debian sid/main amd64 sysstat amd64 12.4.0-1 [600 kB] Get:200 http://127.0.0.1:12990/debian sid/main amd64 parallel all 20161222-1.1 [306 kB] Get:201 http://127.0.0.1:12990/debian sid/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get:202 http://127.0.0.1:12990/debian sid/main amd64 samtools amd64 1.11-1 [545 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 118 MB in 1s (86.9 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 14056 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36-3+b1_amd64.deb ... Unpacking bsdextrautils (2.36-3+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.3-2_amd64.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package libpython3.8-minimal:amd64. Preparing to unpack .../5-libpython3.8-minimal_3.8.6-1_amd64.deb ... Unpacking libpython3.8-minimal:amd64 (3.8.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../7-python3.8-minimal_3.8.6-1_amd64.deb ... Unpacking python3.8-minimal (3.8.6-1) ... Setting up libpython3.8-minimal:amd64 (3.8.6-1) ... Setting up libexpat1:amd64 (2.2.10-1) ... Setting up python3.8-minimal (3.8.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 14903 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.6-1_amd64.deb ... Unpacking python3-minimal (3.8.6-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.64_all.deb ... Unpacking mime-support (3.64) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../2-libncursesw6_6.2+20200918-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.2+20200918-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.0-4_all.deb ... Unpacking readline-common (8.0-4) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.0-4_amd64.deb ... Unpacking libreadline8:amd64 (8.0-4) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../5-libsqlite3-0_3.33.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.33.0-1) ... Selecting previously unselected package libpython3.8-stdlib:amd64. Preparing to unpack .../6-libpython3.8-stdlib_3.8.6-1_amd64.deb ... Unpacking libpython3.8-stdlib:amd64 (3.8.6-1) ... Selecting previously unselected package python3.8. Preparing to unpack .../7-python3.8_3.8.6-1_amd64.deb ... Unpacking python3.8 (3.8.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.8.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.8.6-1) ... Setting up python3-minimal (3.8.6-1) ... Selecting previously unselected package python3. (Reading database ... 15340 files and directories currently installed.) Preparing to unpack .../000-python3_3.8.6-1_amd64.deb ... Unpacking python3 (3.8.6-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../001-libncurses6_6.2+20200918-1_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20200918-1) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../002-libprocps8_2%3a3.3.16-5_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.16-5) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a3.3.16-5_amd64.deb ... Unpacking procps (2:3.3.16-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.12+nmu1_all.deb ... Unpacking sensible-utils (0.0.12+nmu1) ... 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Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up parallel (20161222-1.1) ... Setting up libtabixpp0:amd64 (1.1.0-3) ... Setting up cmake (3.18.4-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:amd64 (8.6.10-1) ... Setting up libpango-1.0-0:amd64 (1.46.2-1) ... Setting up libcairo2:amd64 (1.16.0-4) ... Setting up libvcflib1:amd64 (1.0.1+dfsg-3) ... Setting up libtabixpp-dev:amd64 (1.1.0-3) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-1) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-1) ... Setting up libvcflib-dev:amd64 (1.0.1+dfsg-3) ... Setting up r-base-core (4.0.3-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.3.4-5) ... Setting up r-cran-gtable (0.3.0+dfsg-2) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.20-41-1+b1) ... Setting up r-cran-ps (1.4.0-1) ... Setting up r-cran-nlme (3.1.150-1) ... Setting up r-cran-farver (2.0.3-1+b1) ... Setting up r-cran-viridislite (0.3.0-4) ... Setting up r-cran-r6 (2.4.1-2) ... Setting up r-cran-pkgkitten (0.2.0-1) ... Setting up r-cran-magrittr (1.5-6) ... Setting up r-cran-littler (0.3.12-1) ... Setting up r-cran-rcpp (1.0.5-1) ... Setting up r-cran-rlang (0.4.8-1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up littler (0.3.12-1) ... Setting up r-cran-withr (2.3.0-1) ... Setting up r-cran-backports (1.1.10-1) ... Setting up r-cran-processx (3.4.4-1) ... Setting up r-cran-praise (1.0.0-4) ... Setting up r-cran-digest (0.6.27-1) ... Setting up r-cran-evaluate (0.14-2) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (0.4.1-1+b1) ... Setting up r-cran-mass (7.3-53-1) ... Setting up r-cran-glue (1.4.2-1) ... Setting up r-cran-cli (2.1.0-1) ... Setting up r-cran-lifecycle (0.2.0-2) ... Setting up r-cran-rprojroot (1.3-2-3) ... Setting up r-cran-rstudioapi (0.11-2) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-colorspace (1.4-1+dfsg-2) ... Setting up r-cran-plyr (1.8.6-2) ... Setting up r-cran-rcolorbrewer (1.1-2-3) ... Setting up r-cran-matrix (1.2-18-1+b1) ... Setting up r-cran-mgcv (1.8-33-1) ... Setting up r-cran-ellipsis (0.3.1-1) ... Setting up r-cran-callr (3.5.1-1) ... Setting up r-cran-desc (1.2.0-3) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-scales (1.1.1-1) ... Setting up r-cran-pkgbuild (1.1.0-1) ... Setting up r-cran-vctrs (0.3.4-1) ... Setting up r-cran-pillar (1.4.6-1) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up r-cran-tibble (3.0.4-1) ... Setting up r-cran-testthat (2.3.2-2+b1) ... Setting up r-cran-isoband (0.2.2-1) ... Setting up r-cran-ggplot2 (3.3.2+dfsg-2) ... Setting up libvcflib-tools (1.0.1+dfsg-3) ... Setting up dh-autoreconf (19) ... Setting up debhelper (13.2.1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-4) ... Processing triggers for ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.35.1-2 dpkg-dev_1.20.5 g++-10_10.2.0-15 gcc-10_10.2.0-15 libc6-dev_2.31-4 libstdc++-10-dev_10.2.0-15 libstdc++6_10.2.0-15 linux-libc-dev_5.9.1-1 Package versions: adduser_3.118 apt_2.1.11 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.48 bash_5.1~rc1-2 bc_1.07.1-2+b2 binutils_2.35.1-2 binutils-common_2.35.1-2 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3.0 (quilt) Source: freebayes Binary: freebayes Architecture: any Version: 1.3.2-3 Maintainer: Debian Med Packaging Team Uploaders: Brad Chapman , Andreas Tille Homepage: https://github.com/ekg/freebayes Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/freebayes Vcs-Git: https://salsa.debian.org/med-team/freebayes.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cmake, pkg-config, python3, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel , libvcflib-tools (>= 1.0.0~rc1+dfsg1-6) Package-List: freebayes deb science optional arch=any Checksums-Sha1: cb1ceb2d3996e0f3237515e713829335ff57478b 2641802 freebayes_1.3.2.orig.tar.gz aa11de18a5eeb19b56c57f9ff32d42ad3253d7c3 16540 freebayes_1.3.2-3.debian.tar.xz Checksums-Sha256: 06481ac8b8c2a2fae470ce8806a4d4a7af7b2a81076d092eb6bacb4de2c1ac2f 2641802 freebayes_1.3.2.orig.tar.gz 3cd79de6dd28cffc5efbb15a083cb9b5b7809904380c429834f5397a3aa0c6d7 16540 freebayes_1.3.2-3.debian.tar.xz Files: 08f9c8e7edea344f1f2ae9166d6f1657 2641802 freebayes_1.3.2.orig.tar.gz 0fe5666a7369ad56af230fa217722802 16540 freebayes_1.3.2-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl7UrtsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEwbQ//SNa0N26JHL3Cp/D2WYtu9YIAqUzWUpQp CYdJ1x9zQKBzuucvYLhpugnF/ZBHC+XXzuGyL8SEDjFqHjfTdcjVw5e07a4lkWUd NYKFz1Ww+xnchonNhrcHWSQVVyHaADqfBvR3gVm/N1M8xLS6Y3piX4pOkPqtZ7aH CfeI/zVUgpTixaNk86rvXH3B03W0YyEimRGVQJo/NpZ85a+ps36zr21y8CtwtJqt orSatAQhghh7hzODca8zfvax4PCnpf8/MIwPINDrUwKp1hLLGbyFpL2L6+dm7r36 mn5BjM9yolx2S50bBOUo1TP6L48e0MXFAFKvjaH5fw/Bf25lxyLfb8NM95RnudOR 5Jhh1bqyqZ6jWdxGq9c3uM4Qy+yPyTpK/k+EhH/PIKLyiXSJN2pRRRw307x8RLz+ p42J14T+xWF8o/lQB09EJOK0U//97Bl6AAlxlFcHf7RDZryapsq3VZVmFDslCYPW Hycjr8G3uLwzkTNmfcohTRxlJ15nRhknFhpX4ddG4BdIyL3trXTzT5GDb95uA4qv 6wsVHKJhBhEh9YZtWsZ7q8u4JTkTxtwsefSR69QDqjssNClHXoJvKctyGzewrDZn ZT0TTnb3iDjx+cnxRkBQ2W51MIGop7+FFhH9R0N/qAgqLHh4A3qK8YL76O/50zNI SxAq/pTjZk0= =t6sC -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.QTsINXlW/trustedkeys.kbx': General error gpgv: Signature made Mon Jun 1 07:31:39 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./freebayes_1.3.2-3.dsc dpkg-source: info: extracting freebayes in /<> dpkg-source: info: unpacking freebayes_1.3.2.orig.tar.gz dpkg-source: info: unpacking freebayes_1.3.2-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_libs.patch dpkg-source: info: applying fix_all_target.patch dpkg-source: info: applying fix_test.patch dpkg-source: info: applying vcffirstheader.patch dpkg-source: info: applying skip_failing_test.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying 1ad5cd64ac7270aac03d58d2dba0861ecc85b6b6.patch dpkg-source: info: applying hardening dpkg-source: info: applying version_bump Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-85fc8328-69bd-4f0a-a976-a316ec96ae47 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -b -rfakeroot dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.2-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pranav Ballaney dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/<>' cd src && make clean make[2]: Entering directory '/<>/src' rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp make[2]: Leaving directory '/<>/src' rm -fr bin/* make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- CXXFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64" make -j1 "INSTALL=install --strip-program=true" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64" make[2]: Entering directory '/<>' cd src && make make[3]: Entering directory '/<>/src' DETECTED_VERSION = v1.3.2 CURRENT_VERSION = Updating version file. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c freebayes.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c BedReader.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c CNV.cpp gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -I/usr/include/jsoncpp -c fastlz.c error: invalid argument '-std=gnu++11' not allowed with 'C' make[3]: *** [Makefile:104: fastlz.o] Error 1 make[3]: Leaving directory '/<>/src' make[2]: *** [Makefile:5: all] Error 2 make[2]: Leaving directory '/<>' dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64" returned exit code 2 make[1]: *** [debian/rules:13: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:10: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-10-29T19:47:02Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 11536 Build-Time: 8 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 28 Job: freebayes_1.3.2-3 Machine Architecture: amd64 Package: freebayes Package-Time: 55 Source-Version: 1.3.2-3 Space: 11536 Status: attempted Version: 1.3.2-3 -------------------------------------------------------------------------------- Finished at 2020-10-29T19:47:02Z Build needed 00:00:55, 11536k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 55.596176311s DC-Time-Estimation: 55.596176311 versus expected 128 (r/m: 1.3023166068828105 ; m: 55.596176311)