DC-Build-Header: jellyfish 2.3.0-4 / 2020-05-03 04:13:19 +0000 DC-Task: type:rebuild-binarch-only source:jellyfish version:2.3.0-4 chroot:unstable esttime:464 logfile:/tmp/jellyfish_2.3.0-4_unstable_clang10.log modes:clang10:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang10 jellyfish_2.3.0-4' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-1-44.eu-central-1.compute.internal +==============================================================================+ | jellyfish 2.3.0-4 (amd64) Sun, 03 May 2020 04:13:19 +0000 | +==============================================================================+ Package: jellyfish Version: 2.3.0-4 Source Version: 2.3.0-4 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-2d0f51c8-4476-49af-92c6-02763eddef28' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang10 ------------ + 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 [27.9 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0208.16.pdiff [3982 B] Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-0807.49.pdiff [10.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-1412.30.pdiff [12.9 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-05-02-2007.10.pdiff [13.4 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-05-03-0208.39.pdiff [9476 B] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-05-03-0208.39.pdiff [9476 B] Get:9 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0208.16.pdiff [2772 B] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-0807.49.pdiff [3238 B] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-1412.30.pdiff [7641 B] Get:12 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-02-2007.10.pdiff [10.5 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-03-0208.39.pdiff [18.4 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-05-03-0208.39.pdiff [18.4 kB] Get:14 http://127.0.0.1:12990/debian sid/main Translation-en [6185 kB] Fetched 6480 kB in 2s (4003 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: gcc-10-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libatomic1 libbsd0 libc6-i386 libcc1-0 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libgcc-s1 libgomp1 libitm1 libllvm10 liblsan0 libobjc4 libomp5-10 libquadmath0 libstdc++6 libtsan0 libubsan1 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 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-10-dev libclang-cpp10 libclang1-10 libedit2 libgc1c2 libllvm10 libobjc-9-dev libobjc4 libomp-10-dev libomp5-10 libz3-4 The following packages will be upgraded: gcc-10-base libatomic1 libcc1-0 libgcc-s1 libgomp1 libitm1 liblsan0 libquadmath0 libstdc++6 libtsan0 libubsan1 11 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. Need to get 51.4 MB of archives. After this operation, 259 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libatomic1 amd64 10-20200502-1 [9048 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libubsan1 amd64 10-20200502-1 [134 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libtsan0 amd64 10-20200502-1 [313 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 gcc-10-base amd64 10-20200502-1 [197 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libstdc++6 amd64 10-20200502-1 [492 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libquadmath0 amd64 10-20200502-1 [145 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 liblsan0 amd64 10-20200502-1 [141 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libitm1 amd64 10-20200502-1 [25.7 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libgomp1 amd64 10-20200502-1 [99.3 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libcc1-0 amd64 10-20200502-1 [39.7 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libgcc-s1 amd64 10-20200502-1 [41.2 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.7-4 [6790 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libllvm10 amd64 1:10.0.0-4 [15.5 MB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp10 amd64 1:10.0.0-4 [10.1 MB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200502-1 [41.6 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.3.0-11 [218 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.30-4 [2926 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200502-1 [49.4 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200502-1 [1100 B] Get:23 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200502-1 [510 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-10-dev amd64 1:10.0.0-4 [5062 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libclang1-10 amd64 1:10.0.0-4 [7609 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 clang-10 amd64 1:10.0.0-4 [105 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libomp5-10 amd64 1:10.0.0-4 [338 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 libomp-10-dev amd64 1:10.0.0-4 [85.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.4 MB in 0s (135 MB/s) (Reading database ... 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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 + echo 'g++-9 hold' + dpkg --set-selections + 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 dpkg: warning: package not in status nor available database at line 1: gcc-10 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++-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-10 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 + cd - /build/jellyfish-eov64e + 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 clang version 10.0.0-4 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + clang --version clang version 10.0.0-4 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + cd - /build/jellyfish-eov64e + 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 0 not upgraded. Need to get 1270 kB of archives. After this operation, 4788 kB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.12.5+dfsg-10 [1015 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 5.12.5+dfsg-10 [229 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1270 kB in 0s (19.6 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 ... 12968 files and directories currently installed.) Preparing to unpack .../qt5-qmake-bin_5.12.5+dfsg-10_amd64.deb ... Unpacking qt5-qmake-bin (5.12.5+dfsg-10) ... 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_5.12.5+dfsg-10_amd64.deb ... Unpacking qt5-qmake:amd64 (5.12.5+dfsg-10) ... Setting up qt5-qmake-bin (5.12.5+dfsg-10) ... Setting up qtchooser (66-2) ... Setting up qt5-qmake:amd64 (5.12.5+dfsg-10) ... 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 May 3 04:13 . drwxr-xr-x 75 root root 4096 May 3 04:13 .. -rw-r--r-- 1 root root 276 May 3 04:13 qmake.conf -rw-r--r-- 1 root root 3218 May 3 04:13 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/clang10'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/jellyfish-eov64e/resolver-gNZXcU' 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... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'jellyfish' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/jellyfish.git Please use: git clone https://salsa.debian.org/med-team/jellyfish.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 695 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main jellyfish 2.3.0-4 (dsc) [2567 B] Get:2 http://127.0.0.1:12990/debian sid/main jellyfish 2.3.0-4 (tar) [679 kB] Get:3 http://127.0.0.1:12990/debian sid/main jellyfish 2.3.0-4 (diff) [12.9 kB] Fetched 695 kB in 0s (8594 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/jellyfish-eov64e/jellyfish-2.3.0' with '<>' I: NOTICE: Log filtering will replace 'build/jellyfish-eov64e' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools, 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 [445 B] Get:5 copy:/<>/apt_archive ./ Packages [528 B] Fetched 1930 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 bsdmainutils ca-certificates chrpath d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism dos2unix dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts3 libicu63 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libpipeline1 libprocps8 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libreadline8 librtmp1 libruby2.7 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db mime-support openssl pkg-config po-debconf procps python3 python3-all python3-all-dev python3-dev python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-dev python3.8-minimal rake readline-common ruby ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration samtools sensible-utils swig swig4.0 time yaggo zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support readline-doc ri ruby-dev bundler swig-doc swig-examples swig4.0-examples swig4.0-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl psmisc zip fonts-lato libjs-jquery cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils ca-certificates chrpath d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism dos2unix dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts3 libicu63 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libpipeline1 libprocps8 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libreadline8 librtmp1 libruby2.7 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db mime-support openssl pkg-config po-debconf procps python3 python3-all python3-all-dev python3-dev python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-dev python3.8-minimal rake readline-common ruby ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration samtools sbuild-build-depends-main-dummy sensible-utils swig swig4.0 time yaggo zlib1g-dev 0 upgraded, 106 newly installed, 0 to remove and 0 not upgraded. Need to get 50.5 MB of archives. After this operation, 172 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [960 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.1-1 [1308 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-minimal amd64 3.8.3~rc1-1 [760 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 python3.8-minimal amd64 3.8.3~rc1-1 [1944 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 python3-minimal amd64 3.8.2-3 [37.6 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 mime-support all 3.64 [37.8 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libmpdec2 amd64 2.4.2-3 [84.1 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 readline-common all 8.0-4 [72.5 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.31.1-5 [661 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-stdlib amd64 3.8.3~rc1-1 [1667 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 python3.8 amd64 3.8.3~rc1-1 [415 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libpython3-stdlib amd64 3.8.2-3 [20.8 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 python3 amd64 3.8.2-3 [63.7 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 libncurses6 amd64 6.2-1 [102 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libprocps8 amd64 2:3.3.16-4 [62.7 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 procps amd64 2:3.3.16-4 [262 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 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 1:1.16.2-1 [775 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 1.1.1g-1 [846 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 ca-certificates all 20190110 [157 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 d-shlibs all 0.91 [17.6 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-14 [513 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13 [184 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.8.0-1 [14.8 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.13-5 [151 kB] Get:49 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.64.2-1 [1343 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 libicu63 amd64 63.2-3 [8296 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.10+dfsg-5 [709 kB] Get:52 http://127.0.0.1:12990/debian sid/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:53 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:54 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:55 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:56 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13 [1002 kB] Get:57 http://127.0.0.1:12990/debian sid/main amd64 python3-lib2to3 all 3.8.2-2 [78.4 kB] Get:58 http://127.0.0.1:12990/debian sid/main amd64 python3-distutils all 3.8.2-2 [145 kB] Get:59 http://127.0.0.1:12990/debian sid/main amd64 dh-python all 4.20200315 [91.6 kB] Get:60 http://127.0.0.1:12990/debian sid/main amd64 dos2unix amd64 7.4.0-2 [390 kB] Get:61 http://127.0.0.1:12990/debian sid/main amd64 libbrotli1 amd64 1.0.7-6.1 [267 kB] Get:62 http://127.0.0.1:12990/debian sid/main amd64 libkrb5support0 amd64 1.17-7 [64.4 kB] Get:63 http://127.0.0.1:12990/debian sid/main amd64 libk5crypto3 amd64 1.17-7 [115 kB] Get:64 http://127.0.0.1:12990/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:65 http://127.0.0.1:12990/debian sid/main amd64 libkrb5-3 amd64 1.17-7 [366 kB] Get:66 http://127.0.0.1:12990/debian sid/main amd64 libgssapi-krb5-2 amd64 1.17-7 [156 kB] Get:67 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [69.0 kB] Get:68 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [106 kB] Get:69 http://127.0.0.1:12990/debian sid/main amd64 libldap-common all 2.4.50+dfsg-1 [92.9 kB] Get:70 http://127.0.0.1:12990/debian sid/main amd64 libldap-2.4-2 amd64 2.4.50+dfsg-1 [228 kB] Get:71 http://127.0.0.1:12990/debian sid/main amd64 libnghttp2-14 amd64 1.40.0-1 [85.0 kB] Get:72 http://127.0.0.1:12990/debian sid/main amd64 libpsl5 amd64 0.21.0-1 [55.1 kB] Get:73 http://127.0.0.1:12990/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b1 [60.8 kB] Get:74 http://127.0.0.1:12990/debian sid/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:75 http://127.0.0.1:12990/debian sid/main amd64 libcurl3-gnutls amd64 7.68.0-1 [319 kB] Get:76 http://127.0.0.1:12990/debian sid/main amd64 libdeflate0 amd64 1.5-3 [55.8 kB] Get:77 http://127.0.0.1:12990/debian sid/main amd64 libexpat1-dev amd64 2.2.9-1 [136 kB] Get:78 http://127.0.0.1:12990/debian sid/main amd64 libhts3 amd64 1.10.2-3 [370 kB] Get:79 http://127.0.0.1:12990/debian sid/main amd64 liblzma-dev amd64 5.2.4-1+b1 [211 kB] Get:80 http://127.0.0.1:12990/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:81 http://127.0.0.1:12990/debian sid/main amd64 libhts-dev amd64 1.10.2-3 [4846 kB] Get:82 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8 amd64 3.8.3~rc1-1 [1620 kB] Get:83 http://127.0.0.1:12990/debian sid/main amd64 libpython3.8-dev amd64 3.8.3~rc1-1 [3930 kB] Get:84 http://127.0.0.1:12990/debian sid/main amd64 libpython3-dev amd64 3.8.2-3 [21.0 kB] Get:85 http://127.0.0.1:12990/debian sid/main amd64 libpython3-all-dev amd64 3.8.2-3 [1068 B] Get:86 http://127.0.0.1:12990/debian sid/main amd64 rubygems-integration all 1.16 [5632 B] Get:87 http://127.0.0.1:12990/debian sid/main amd64 ruby2.7 amd64 2.7.0-6 [652 kB] Get:88 http://127.0.0.1:12990/debian sid/main amd64 ruby amd64 1:2.7+1 [11.5 kB] Get:89 http://127.0.0.1:12990/debian sid/main amd64 rake all 13.0.1-4 [84.7 kB] Get:90 http://127.0.0.1:12990/debian sid/main amd64 ruby-minitest all 5.13.0-1 [57.3 kB] Get:91 http://127.0.0.1:12990/debian sid/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get:92 http://127.0.0.1:12990/debian sid/main amd64 ruby-power-assert all 1.1.7-1 [11.4 kB] Get:93 http://127.0.0.1:12990/debian sid/main amd64 ruby-test-unit all 3.3.5-1 [85.3 kB] Get:94 http://127.0.0.1:12990/debian sid/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get:95 http://127.0.0.1:12990/debian sid/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:96 http://127.0.0.1:12990/debian sid/main amd64 libruby2.7 amd64 2.7.0-6 [4083 kB] Get:97 http://127.0.0.1:12990/debian sid/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get:98 http://127.0.0.1:12990/debian sid/main amd64 python3-all amd64 3.8.2-3 [1056 B] Get:99 http://127.0.0.1:12990/debian sid/main amd64 python3.8-dev amd64 3.8.3~rc1-1 [514 kB] Get:100 http://127.0.0.1:12990/debian sid/main amd64 python3-dev amd64 3.8.2-3 [1164 B] Get:101 http://127.0.0.1:12990/debian sid/main amd64 python3-all-dev amd64 3.8.2-3 [1064 B] Get:102 http://127.0.0.1:12990/debian sid/main amd64 samtools amd64 1.10-3 [523 kB] Get:103 http://127.0.0.1:12990/debian sid/main amd64 swig4.0 amd64 4.0.1-5 [1402 kB] Get:104 http://127.0.0.1:12990/debian sid/main amd64 swig all 4.0.1-5 [329 kB] Get:105 http://127.0.0.1:12990/debian sid/main amd64 time amd64 1.7-25.1+b1 [31.6 kB] Get:106 http://127.0.0.1:12990/debian sid/main amd64 yaggo all 1.5.10-2 [18.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 50.5 MB in 0s (109 MB/s) Selecting previously unselected package bsdmainutils. 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Selecting previously unselected package libruby2.7:amd64. Preparing to unpack .../76-libruby2.7_2.7.0-6_amd64.deb ... Unpacking libruby2.7:amd64 (2.7.0-6) ... Selecting previously unselected package pkg-config. Preparing to unpack .../77-pkg-config_0.29.2-1_amd64.deb ... Unpacking pkg-config (0.29.2-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../78-python3-all_3.8.2-3_amd64.deb ... Unpacking python3-all (3.8.2-3) ... Selecting previously unselected package python3.8-dev. Preparing to unpack .../79-python3.8-dev_3.8.3~rc1-1_amd64.deb ... Unpacking python3.8-dev (3.8.3~rc1-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../80-python3-dev_3.8.2-3_amd64.deb ... Unpacking python3-dev (3.8.2-3) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../81-python3-all-dev_3.8.2-3_amd64.deb ... Unpacking python3-all-dev (3.8.2-3) ... Selecting previously unselected package samtools. 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Setting up libpsl5:amd64 (0.21.0-1) ... Setting up mime-support (3.64) ... Setting up ruby-power-assert (1.1.7-1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.2-1) ... Setting up libglib2.0-0:amd64 (2.64.2-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13) ... Setting up libbrotli1:amd64 (1.0.7-6.1) ... Setting up libsqlite3-0:amd64 (3.31.1-5) ... Setting up libnghttp2-14:amd64 (1.40.0-1) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up libdeflate0 (1.5-3) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.50+dfsg-1) ... Setting up libicu63:amd64 (63.2-3) ... Setting up libkrb5support0:amd64 (1.17-7) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Setting up ruby-minitest (5.13.0-1) ... Setting up autotools-dev (20180224.1) ... Setting up libexpat1-dev:amd64 (2.2.9-1) ... Setting up ruby-test-unit (3.3.5-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b1) ... Setting up libncurses6:amd64 (6.2-1) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-10) ... Setting up pkg-config (0.29.2-1) ... Setting up d-shlibs (0.91) ... Setting up libk5crypto3:amd64 (1.17-7) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2) ... Setting up liblzma-dev:amd64 (5.2.4-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-7) ... Setting up dos2unix (7.4.0-2) ... Setting up libmpdec2:amd64 (2.4.2-3) ... Setting up swig4.0 (4.0.1-5) ... Setting up openssl (1.1.1g-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (8.0-4) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:amd64 (2.9.10+dfsg-5) ... Setting up chrpath (0.16-2+b1) ... Setting up libprocps8:amd64 (2:3.3.16-4) ... Setting up libfile-stripnondeterminism-perl (1.8.0-1) ... Setting up swig (4.0.1-5) ... Setting up libtool (2.4.6-14) ... Setting up libreadline8:amd64 (8.0-4) ... Setting up bc (1.07.1-2+b2) ... Setting up libldap-2.4-2:amd64 (2.4.50+dfsg-1) ... Setting up m4 (1.4.18-4) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libgssapi-krb5-2:amd64 (1.17-7) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up procps (2:3.3.16-4) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libpython3.8-stdlib:amd64 (3.8.3~rc1-1) ... Setting up python3.8 (3.8.3~rc1-1) ... Setting up libpython3-stdlib:amd64 (3.8.2-3) ... Setting up automake (1:1.16.2-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up libcurl3-gnutls:amd64 (7.68.0-1) ... Setting up python3 (3.8.2-3) ... Setting up rubygems-integration (1.16) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython3.8:amd64 (3.8.3~rc1-1) ... Setting up python3-lib2to3 (3.8.2-2) ... Setting up python3-distutils (3.8.2-2) ... Setting up dh-python (4.20200315) ... Setting up libhts3:amd64 (1.10.2-3) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.10.2-3) ... Setting up python3-all (3.8.2-3) ... Setting up samtools (1.10-3) ... Setting up libpython3.8-dev:amd64 (3.8.3~rc1-1) ... Setting up python3.8-dev (3.8.3~rc1-1) ... Setting up libpython3-dev:amd64 (3.8.2-3) ... Setting up libpython3-all-dev:amd64 (3.8.2-3) ... Setting up python3-dev (3.8.2-3) ... Setting up python3-all-dev (3.8.2-3) ... Setting up ruby2.7 (2.7.0-6) ... Setting up debhelper (13) ... Setting up dh-autoreconf (19) ... Setting up ruby (1:2.7+1) ... Setting up rake (13.0.1-4) ... Setting up yaggo (1.5.10-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libruby2.7:amd64 (2.7.0-6) ... Processing triggers for libc-bin (2.30-4) ... Processing triggers for ca-certificates (20190110) ... 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 amd64) +------------------------------------------------------------------------------+ | 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_2.34-6 dpkg-dev_1.19.7 g++-9_9.3.0-11 gcc-9_9.3.0-11 libc6-dev_2.30-4 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200502-1 linux-libc-dev_5.6.7-1 Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 bc_1.07.1-2+b2 binutils_2.34-6 binutils-common_2.34-6 binutils-x86-64-linux-gnu_2.34-6 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 chrpath_0.16-2+b1 clang-10_1:10.0.0-4 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.3.0-11 d-shlibs_0.91 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20200315 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dos2unix_7.4.0-2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.3.0-11 gcc_4:9.2.1-3.1 gcc-10-base_10-20200502-1 gcc-9_9.3.0-11 gcc-9-base_9.3.0-11 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_10-20200502-1 lib32gcc1_1:10-20200502-1 lib32stdc++6_10-20200502-1 libacl1_2.2.53-8 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libasan5_9.3.0-11 libatomic1_10-20200502-1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbinutils_2.34-6 libblkid1_2.34-0.1 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4 libc-dev-bin_2.30-4 libc6_2.30-4 libc6-dev_2.30-4 libc6-i386_2.30-4 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10-20200502-1 libclang-common-10-dev_1:10.0.0-4 libclang-cpp10_1:10.0.0-4 libclang1-10_1:10.0.0-4 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-6 libctf0_2.34-6 libcurl3-gnutls_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_13 libdeflate0_1.5-3 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgc1c2_1:7.6.4-0.4 libgcc-9-dev_9.3.0-11 libgcc-s1_10-20200502-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200502-1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libitm1_10-20200502-1 libk5crypto3_1.17-7 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7 libkrb5support0_1.17-7 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 libllvm10_1:10.0.0-4 liblsan0_10-20200502-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1+b1 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libobjc-9-dev_9.3.0-11 libobjc4_10-20200502-1 libomp-10-dev_1:10.0.0-4 libomp5-10_1:10.0.0-4 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libprocps8_2:3.3.16-4 libpsl5_0.21.0-1 libpython3-all-dev_3.8.2-3 libpython3-dev_3.8.2-3 libpython3-stdlib_3.8.2-3 libpython3.8_3.8.3~rc1-1 libpython3.8-dev_3.8.3~rc1-1 libpython3.8-minimal_3.8.3~rc1-1 libpython3.8-stdlib_3.8.3~rc1-1 libquadmath0_10-20200502-1 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libruby2.7_2.7.0-6 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+b1 libselinux1_3.0-1+b3 libsemanage-common_3.0-1 libsemanage1_3.0-1+b3 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-11 libstdc++6_10-20200502-1 libsub-override-perl_0.09-2 libsystemd0_245.5-2 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10-20200502-1 libubsan1_10-20200502-1 libuchardet0_0.0.6-3 libudev1_245.5-2 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-5 libyaml-0-2_0.2.2-1 libz3-4_4.8.7-4 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.6.7-1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.3 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1g-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 pkg-config_0.29.2-1 po-debconf_1.0.21 procps_2:3.3.16-4 python3_3.8.2-3 python3-all_3.8.2-3 python3-all-dev_3.8.2-3 python3-dev_3.8.2-3 python3-distutils_3.8.2-2 python3-lib2to3_3.8.2-2 python3-minimal_3.8.2-3 python3.8_3.8.3~rc1-1 python3.8-dev_3.8.3~rc1-1 python3.8-minimal_3.8.3~rc1-1 qt5-qmake_5.12.5+dfsg-10 qt5-qmake-bin_5.12.5+dfsg-10 qtchooser_66-2 rake_13.0.1-4 readline-common_8.0-4 ruby_1:2.7+1 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-1 ruby-test-unit_3.3.5-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.0-6 rubygems-integration_1.16 samtools_1.10-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 swig_4.0.1-5 swig4.0_4.0.1-5 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 time_1.7-25.1+b1 tzdata_2020a-1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 yaggo_1.5.10-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: jellyfish Binary: jellyfish, libjellyfish-2.0-2, libjellyfish-2.0-dev, python3-dna-jellyfish, libjellyfish-perl, jellyfish-examples Architecture: amd64 Version: 2.3.0-4 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille , Michael R. Crusoe Homepage: https://www.cbcb.umd.edu/software/jellyfish/ Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 12), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools Package-List: jellyfish deb science optional arch=amd64 jellyfish-examples deb science optional arch=amd64 libjellyfish-2.0-2 deb libs optional arch=amd64 libjellyfish-2.0-dev deb libdevel optional arch=amd64 libjellyfish-perl deb perl optional arch=amd64 python3-dna-jellyfish deb python optional arch=amd64 Checksums-Sha1: 4f7f5263e6e097c623531a660ef6158e2fb5e17b 679125 jellyfish_2.3.0.orig.tar.gz 22e9bc1bbc48c53234b8ff9424a26e3a72325e2b 12864 jellyfish_2.3.0-4.debian.tar.xz Checksums-Sha256: 29ead991de90151dbe4a2717f7ac30b3852296c9cbdda8b001121a1f2fa714db 679125 jellyfish_2.3.0.orig.tar.gz 65efcd70726d6b0cc826fe8c28bcfaaef1cdff58d95bc4e6fb1006fd55bb38ca 12864 jellyfish_2.3.0-4.debian.tar.xz Files: b447a26df0f1e11526129907a9b0acdb 679125 jellyfish_2.3.0.orig.tar.gz 996463396e4f33335f384010ff633b19 12864 jellyfish_2.3.0-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl33oMAACgkQPCZ2P2xn 5uJNlxAAi68HluXwi1iCEb2G89aHcAXEdvkYb9rEg6PF2pVLJ7CXlLjyUKRg1xBw //N6C/XoU3NBVFXP1uoUAQ+j1dQsBAWPBl7e9c/O/gu1RbUdzHmS3/xsm0xtt4yz PIxxkVc2b3V7ZRbNdvmgU2r/heHxcQNkl+yyooG3mDkj+REpIxeIARs7WBzCKoX/ 4sz9NC4yv+aeOYU+Rg1S9xNy0IH7sYUGjIrA0bSq+kNnGIkHS1HGuk9uPXA0Su7J MZoxa/kKC641pjym6xTFmcmbVT8emR+7xWUwQAnDveXVxjv44c2OLHQIYXpwLZFn OUChNcSAbHwXjMgacJFva6uoTCxVFYocLa9EBY61J5JBmff1N+RdNdj1sQC2MPuf D0D5b5t4F6am1A79lG9pWSB2bnXBCFp+WnrQ1LR6Ctx/42MlxGlSppPe0kW7kyqB w/emDObvzlxS0QXk9Ye/r2mFZg4uyl4n17BOxxH5SCM62MzG71gkTZvOwDlo9EHW hxfhpbqBtZtwvu5lMgibgieTsv/LnMgdLv2JFw6zv7vk1hyNdHIbaMhHOI65s8Wq BQl9mQDepIFgUaOFvQJIlrzQaPRXHgG9JccF8EEzOXLg0764GHKIXM7K1g/DMXg6 ou8PQjltJphJbJudVQ9IiN/QPf4FwiZKF1GIsPXWLL8Fh3Lp5T0= =L3Fb -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Dec 16 15:20:32 2019 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./jellyfish_2.3.0-4.dsc dpkg-source: info: extracting jellyfish in /<> dpkg-source: info: unpacking jellyfish_2.3.0.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying manpage_whatis_entry.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying fix_replacement_of_-L_option.patch dpkg-source: info: applying test_needs_bash dpkg-source: info: applying python3 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-2d0f51c8-4476-49af-92c6-02763eddef28 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 jellyfish dpkg-buildpackage: info: source version 2.3.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi rm -f tests/compat.sh rm -f swig/python/jellyfish* # swig/python/dna_jellyfish.py rm -f swig/perl5/blib/arch/auto/jellyfish/jellyfish.so rm -f swig/perl5/blib/bin/.exists rm -f swig/perl5/blib/lib/.exists rm -f swig/perl5/blib/lib/auto/jellyfish/.exists rm -f swig/perl5/blib/man1/.exists rm -f swig/perl5/blib/man3/.exists rm -f swig/perl5/blib/script/.exists rm -f swig/perl5/jellyfish.bs rm -f swig/perl5/pm_to_blib rm -rf swig/perl5/MYMETA.json swig/perl5/MYMETA.yml swig/perl5/Makefile swig/perl5/blib/ make[1]: Leaving directory '/<>' debian/rules build dh build --with python3 dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 configure: WARNING: unrecognized options: --disable-maintainer-mode checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld used by gcc... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for htslib... yes checking for samtools... /usr/bin/samtools checking for unix2dos... /usr/bin/unix2dos checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... d:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:0:0:0 checking for x86 cpuid 0x00000001 output... 50657:40800:fffa3203:1f8bfbff checking for x86 cpuid 0x00000007 output... 0:d19f47ab:18:0 checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800 checking for x86-AVX xgetbv 0x00000000 output... 2ff:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C++ compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... yes checking whether ADX is supported by the processor and OS... yes checking whether C++ compiler accepts -madx... yes checking whether MPX is supported by the processor... yes checking whether MPX is supported by the processor and OS... yes checking whether C++ compiler accepts -mmpx... yes checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C++ compiler accepts -mabm... no configure: WARNING: Your processor and OS supports ABM instructions but not your compiler, can you try another compiler? checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C++ compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C++ compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... no checking whether SHA is supported by the processor... no checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C++ compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... yes checking whether AVX512-F is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx512f... yes checking whether AVX512-CD is supported by the processor... yes checking whether AVX512-CD is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx512cd... yes checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... yes checking whether AVX512-VL is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx512vl... yes checking whether AVX512-BW is supported by the processor... yes checking whether AVX512-BW is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx512bw... yes checking whether AVX512-DQ is supported by the processor... yes checking whether AVX512-DQ is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx512dq... yes checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for __int128... yes checking for std::numeric_limits<__int128>... no checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... yes checking for swig... /usr/bin/swig checking SWIG version... 4.0.1 checking for SWIG library... /usr/share/swig4.0 checking for python... /usr/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python3.8 checking for Python library path... -L/usr/lib -lpython3.8 checking for Python site-packages path... /usr/lib/python3/dist-packages checking python extra libraries... -lcrypt -lpthread -ldl -lutil -lm -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for perl... /usr/bin/perl checking for Perl prefix... /usr checking for Perl extension include path... /usr/lib/x86_64-linux-gnu/perl/5.30/CORE checking for Perl extension target directory... /usr/lib/perl/5.30.0 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_configure --sourcedirectory=swig/perl5 cd swig/perl5 && perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread" -I/<>/debian/tmp//usr/include/jellyfish-2.3.0 -L/<>/debian/tmp//usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -L/<>/debian/tmp//usr/lib/x86_64-linux-gnu Warning (mostly harmless): No library found for -ljellyfish-2.0 Generating a Unix-style Makefile Writing Makefile for jellyfish Writing MYMETA.yml and MYMETA.json dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:217: python3.8 setup.py config running config make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam make[2]: Entering directory '/<>' /usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo /usr/bin/swig -c++ -python -I./../include -o swig/python/swig_wrap.cpp swig/jellyfish.i /usr/bin/swig -c++ -perl5 -I./../include -o swig/perl5/swig_wrap.cpp swig/jellyfish.i make all-am make[3]: Entering directory '/<>' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/count_main.o sub_commands/count_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/info_main.o sub_commands/info_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/dump_main.o sub_commands/dump_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/histo_main.o sub_commands/histo_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/stats_main.o sub_commands/stats_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/merge_main.o sub_commands/merge_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/bc_main.o sub_commands/bc_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/query_main.o sub_commands/query_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/cite_main.o sub_commands/cite_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 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--mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/misc.lo lib/misc.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c lib/misc.cc -fPIC -DPIC -o lib/.libs/misc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c lib/misc.cc -o lib/misc.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/int128.lo lib/int128.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c lib/int128.cc -fPIC -DPIC -o lib/.libs/int128.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c lib/int128.cc -o lib/int128.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/thread_exec.lo lib/thread_exec.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c lib/thread_exec.cc -fPIC -DPIC -o lib/.libs/thread_exec.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c lib/thread_exec.cc -o lib/thread_exec.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o lib/jsoncpp.lo lib/jsoncpp.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c lib/jsoncpp.cpp -fPIC -DPIC -o lib/.libs/jsoncpp.o lib/jsoncpp.cpp:2303:74: error: implicit conversion from 'const Json::Int64' (aka 'const long long') to 'double' changes value from 9223372036854775807 to 9223372036854775808 [-Werror,-Wimplicit-int-float-conversion] JSON_ASSERT_MESSAGE( value_.real_ >= minInt64 && value_.real_ <= maxInt64, "Real out of Int64 range" ); ~~ ^~~~~~~~ lib/jsoncpp.cpp:1566:58: note: expanded from macro 'JSON_ASSERT_MESSAGE' #define JSON_ASSERT_MESSAGE( condition, message ) if (!( condition )) JSON_FAIL_MESSAGE( message ) ^~~~~~~~~ lib/jsoncpp.cpp:2331:67: error: implicit conversion from 'const Json::UInt64' (aka 'const unsigned long long') to 'double' changes value from 18446744073709551615 to 18446744073709551616 [-Werror,-Wimplicit-int-float-conversion] JSON_ASSERT_MESSAGE( value_.real_ >= 0 && value_.real_ <= maxUInt64, "Real out of UInt64 range" ); ~~ ^~~~~~~~~ lib/jsoncpp.cpp:1566:58: note: expanded from macro 'JSON_ASSERT_MESSAGE' #define JSON_ASSERT_MESSAGE( condition, message ) if (!( condition )) JSON_FAIL_MESSAGE( message ) ^~~~~~~~~ 2 errors generated. make[3]: *** [Makefile:2149: lib/jsoncpp.lo] Error 1 make[3]: Leaving directory '/<>' make[2]: *** [Makefile:1025: all] Error 2 make[2]: Leaving directory '/<>' dh_auto_build: error: make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam returned exit code 2 make[1]: *** [debian/rules:75: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:21: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-05-03T04:14:27Z 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: 18432 Build-Time: 39 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 14 Job: jellyfish_2.3.0-4 Machine Architecture: amd64 Package: jellyfish Package-Time: 68 Source-Version: 2.3.0-4 Space: 18432 Status: attempted Version: 2.3.0-4 -------------------------------------------------------------------------------- Finished at 2020-05-03T04:14:27Z Build needed 00:01:08, 18432k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 68.808160455s DC-Time-Estimation: 68.808160455 versus expected 464 (r/m: 5.743386204946612 ; m: 68.808160455)