DC-Build-Header: libmems 1.6.0+4725-8 / 2020-02-25 14:00:55 +0000 DC-Task: type:rebuild-binarch-only source:libmems version:1.6.0+4725-8 chroot:unstable esttime:435 logfile:/tmp/libmems_1.6.0+4725-8_unstable_clang8.log modes:clang8:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang8 libmems_1.6.0+4725-8' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-4-228.eu-central-1.compute.internal +==============================================================================+ | libmems 1.6.0+4725-8 (amd64) Tue, 25 Feb 2020 14:00:56 +0000 | +==============================================================================+ Package: libmems Version: 1.6.0+4725-8 Source Version: 1.6.0+4725-8 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-ef459e55-f0c9-4d15-b1b8-f1db17e7a577' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang8 ----------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=8 + echo 'Install of clang-8' Install of clang-8 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [142 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 2020-02-24-0823.32.pdiff [11.0 kB] Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-1420.34.pdiff [30.2 kB] Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-2014.03.pdiff [16.9 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0213.11.pdiff [23.2 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0815.22.pdiff [9222 B] Get:9 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-0823.32.pdiff [15.5 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-1420.34.pdiff [27.5 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-2014.03.pdiff [21.6 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0213.11.pdiff [35.0 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0815.22.pdiff [9222 B] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0815.22.pdiff [20.1 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0815.22.pdiff [20.1 kB] Get:14 http://127.0.0.1:12990/debian sid/main Translation-en [6195 kB] Fetched 6604 kB in 2s (3691 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-8 libomp-8-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: cpp-9 g++-9 gcc-8-base gcc-9 gcc-9-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libgcc-8-dev libgcc-9-dev libllvm8 libmpx2 libobjc-8-dev libobjc4 libomp5-8 libstdc++-8-dev libstdc++-9-dev Suggested packages: clang-8-doc gcc-9-locales g++-9-multilib gcc-9-doc gcc-9-multilib libomp-8-doc libstdc++-8-doc libstdc++-9-doc Recommended packages: llvm-8-dev python3 The following NEW packages will be installed: clang-8 gcc-8-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libgcc-8-dev libllvm8 libmpx2 libobjc-8-dev libobjc-9-dev libobjc4 libomp-8-dev libomp5-8 libstdc++-8-dev The following packages will be upgraded: cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libgcc-9-dev libstdc++-9-dev 7 upgraded, 20 newly installed, 0 to remove and 2 not upgraded. Need to get 74.9 MB of archives. After this operation, 223 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.2.1-30 [389 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 g++-9 amd64 9.2.1-30 [10.7 MB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 gcc-9 amd64 9.2.1-30 [10.0 MB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libstdc++-9-dev amd64 9.2.1-30 [1697 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.2.1-30 [2349 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 cpp-9 amd64 9.2.1-30 [9711 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 gcc-9-base amd64 9.2.1-30 [196 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libllvm8 amd64 1:8.0.1-7 [13.8 MB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 gcc-8-base amd64 8.3.0-29 [194 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libmpx2 amd64 8.3.0-29 [11.4 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libgcc-8-dev amd64 8.3.0-29 [2297 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libstdc++-8-dev amd64 8.3.0-29 [1543 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200222-1 [41.6 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libobjc-8-dev amd64 8.3.0-29 [227 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.29-10 [2918 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200222-1 [49.4 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200222-1 [1104 B] Get:21 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200222-1 [510 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-8-dev amd64 1:8.0.1-7 [2989 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 libclang1-8 amd64 1:8.0.1-7 [6244 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 clang-8 amd64 1:8.0.1-7 [8010 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.2.1-30 [219 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 libomp5-8 amd64 1:8.0.1-7 [331 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libomp-8-dev amd64 1:8.0.1-7 [62.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.9 MB in 1s (101 MB/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 ... 12119 files and directories currently installed.) Preparing to unpack .../00-libasan5_9.2.1-30_amd64.deb ... Unpacking libasan5:amd64 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../01-g++-9_9.2.1-30_amd64.deb ... Unpacking g++-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../02-gcc-9_9.2.1-30_amd64.deb ... Unpacking gcc-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../03-libstdc++-9-dev_9.2.1-30_amd64.deb ... 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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++-8 g++-4.6 + ln -s clang-8 gcc-4.6 + ln -s clang-8 cpp-4.6 + ln -s clang-8 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++-8 g++-4.7 + ln -s clang-8 gcc-4.7 + ln -s clang-8 cpp-4.7 + ln -s clang-8 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++-8 g++-4.8 + ln -s clang-8 gcc-4.8 + ln -s clang-8 cpp-4.8 + ln -s clang-8 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++-8 g++-4.9 + ln -s clang-8 gcc-4.9 + ln -s clang-8 cpp-4.9 + ln -s clang-8 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++-8 g++-5 + ln -s clang-8 gcc-5 + ln -s clang-8 cpp-5 + ln -s clang-8 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++-8 g++-6 + ln -s clang-8 gcc-6 + ln -s clang-8 cpp-6 + ln -s clang-8 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++-8 g++-7 + ln -s clang-8 gcc-7 + ln -s clang-8 cpp-7 + ln -s clang-8 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++-8 g++-8 + ln -s clang-8 gcc-8 + ln -s clang-8 cpp-8 + ln -s clang-8 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++-8 g++-9 + ln -s clang-8 gcc-9 + ln -s clang-8 cpp-9 + ln -s clang-8 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++-8 g++-10 + ln -s clang-8 gcc-10 + ln -s clang-8 cpp-10 + ln -s clang-8 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/libmems-uDGH5d + 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 I: Finished running '/tmp/clang8'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/libmems-uDGH5d/resolver-3nFCjs' 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: libgmp10 zlib1g 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 343 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 libgmp10 amd64 2:6.2.0+dfsg-4 [253 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-2 [90.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 343 kB in 0s (6434 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 ... 13887 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.2.0+dfsg-4_amd64.deb ... Unpacking libgmp10:amd64 (2:6.2.0+dfsg-4) over (2:6.2.0+dfsg-3) ... Setting up libgmp10:amd64 (2:6.2.0+dfsg-4) ... (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 ... 13887 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-2_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-2) over (1:1.2.11.dfsg-1.2) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-2) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'libmems' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libmems.git Please use: git clone https://salsa.debian.org/med-team/libmems.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 248 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main libmems 1.6.0+4725-8 (dsc) [2168 B] Get:2 http://127.0.0.1:12990/debian sid/main libmems 1.6.0+4725-8 (tar) [237 kB] Get:3 http://127.0.0.1:12990/debian sid/main libmems 1.6.0+4725-8 (diff) [8696 B] Fetched 248 kB in 0s (3400 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/libmems-uDGH5d/libmems-1.6.0+4725' with '<>' I: NOTICE: Log filtering will replace 'build/libmems-uDGH5d' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), d-shlibs, pkg-config, libgenome-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-dev, build-essential, fakeroot Filtered Build-Depends: debhelper (>= 11~), d-shlibs, pkg-config, libgenome-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-dev, 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 [430 B] Get:5 copy:/<>/apt_archive ./ Packages [513 B] Fetched 1900 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 bsdmainutils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.67-dev libboost-filesystem1.67.0 libboost-iostreams-dev libboost-iostreams1.67-dev libboost-iostreams1.67.0 libboost-program-options-dev libboost-program-options1.67-dev libboost-program-options1.67.0 libboost-regex1.67-dev libboost-regex1.67.0 libboost-system1.67-dev libboost-system1.67.0 libboost1.67-dev libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libgenome-dev libgenome0 libglib2.0-0 libicu-dev libicu63 libmagic-mgc libmagic1 libmuscle-dev libmuscle1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev libboost-contract1.67-dev libboost-coroutine1.67-dev libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev libboost-graph1.67-dev libboost-graph-parallel1.67-dev libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev libboost-python1.67-dev libboost-random1.67-dev libboost-serialization1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-test1.67-dev libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev icu-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.67-dev libboost-filesystem1.67.0 libboost-iostreams-dev libboost-iostreams1.67-dev libboost-iostreams1.67.0 libboost-program-options-dev libboost-program-options1.67-dev libboost-program-options1.67.0 libboost-regex1.67-dev libboost-regex1.67.0 libboost-system1.67-dev libboost-system1.67.0 libboost1.67-dev libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libgenome-dev libgenome0 libglib2.0-0 libicu-dev libicu63 libmagic-mgc libmagic1 libmuscle-dev libmuscle1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. 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http://127.0.0.1:12990/debian sid/main amd64 debhelper all 12.9 [994 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 icu-devtools amd64 63.2-2 [189 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 libboost1.67-dev amd64 1.67.0-17 [8389 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 libboost-system1.67.0 amd64 1.67.0-17 [229 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 libboost-filesystem1.67.0 amd64 1.67.0-17 [260 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 libboost-system1.67-dev amd64 1.67.0-17 [232 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 libboost-filesystem1.67-dev amd64 1.67.0-17 [269 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 libboost-filesystem-dev amd64 1.67.0.2+b1 [4312 B] Get:43 http://127.0.0.1:12990/debian sid/main amd64 libboost-regex1.67.0 amd64 1.67.0-17 [513 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 libicu-dev amd64 63.2-2 [9190 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libboost-regex1.67-dev amd64 1.67.0-17 [567 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 libboost-iostreams1.67.0 amd64 1.67.0-17 [250 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 libboost-iostreams1.67-dev amd64 1.67.0-17 [256 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 libboost-iostreams-dev amd64 1.67.0.2+b1 [4260 B] Get:49 http://127.0.0.1:12990/debian sid/main amd64 libboost-program-options1.67.0 amd64 1.67.0-17 [356 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 libboost-program-options1.67-dev amd64 1.67.0-17 [381 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 libboost-program-options-dev amd64 1.67.0.2+b1 [4288 B] Get:52 http://127.0.0.1:12990/debian sid/main amd64 libgenome0 amd64 1.3.11+svn20110227.4616-2 [118 kB] Get:53 http://127.0.0.1:12990/debian sid/main amd64 libgenome-dev amd64 1.3.11+svn20110227.4616-2 [183 kB] Get:54 http://127.0.0.1:12990/debian sid/main amd64 libmuscle1 amd64 3.7+4565-6 [255 kB] Get:55 http://127.0.0.1:12990/debian sid/main amd64 libmuscle-dev amd64 3.7+4565-6 [304 kB] Get:56 http://127.0.0.1:12990/debian sid/main amd64 pkg-config amd64 0.29-6 [63.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 41.2 MB in 0s (91.5 MB/s) Selecting previously unselected package bsdmainutils. 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Setting up libboost-program-options1.67.0:amd64 (1.67.0-17) ... Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up libgenome0:amd64 (1.3.11+svn20110227.4616-2) ... Setting up libmuscle1 (3.7+4565-6) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libgenome-dev (1.3.11+svn20110227.4616-2) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libboost-program-options1.67-dev:amd64 (1.67.0-17) ... Setting up libglib2.0-0:amd64 (2.62.4-2) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.9) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libicu63:amd64 (63.2-2) ... Setting up autotools-dev (20180224.1) ... Setting up libboost-program-options-dev:amd64 (1.67.0.2+b1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libmuscle-dev (3.7+4565-6) ... 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 icu-devtools (63.2-2) ... Setting up pkg-config (0.29-6) ... Setting up libboost-iostreams1.67.0:amd64 (1.67.0-17) ... Setting up d-shlibs (0.88) ... 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 libboost-system1.67.0:amd64 (1.67.0-17) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libicu-dev:amd64 (63.2-2) ... Setting up libxml2:amd64 (2.9.10+dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libboost-regex1.67.0:amd64 (1.67.0-17) ... Setting up libtool (2.4.6-13) ... Setting up libboost-regex1.67-dev:amd64 (1.67.0-17) ... Setting up m4 (1.4.18-4) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up libboost-filesystem1.67.0:amd64 (1.67.0-17) ... Setting up libboost-system1.67-dev:amd64 (1.67.0-17) ... Setting up libboost-iostreams1.67-dev:amd64 (1.67.0-17) ... Setting up automake (1:1.16.1-4) ... 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 libboost-filesystem1.67-dev:amd64 (1.67.0-17) ... Setting up libboost-iostreams-dev:amd64 (1.67.0.2+b1) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libboost-filesystem-dev:amd64 (1.67.0.2+b1) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.9) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | 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_2.34-3 dpkg-dev_1.19.7 g++-9_9.2.1-30 gcc-9_9.2.1-30 libc6-dev_2.29-10 libstdc++-8-dev_8.3.0-29 libstdc++-9-dev_9.2.1-30 libstdc++6_10-20200222-1 linux-libc-dev_5.4.19-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-5 binutils_2.34-3 binutils-common_2.34-3 binutils-x86-64-linux-gnu_2.34-3 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 clang-8_1:8.0.1-7 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.2.1-30 d-shlibs_0.88 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 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_9.2.1-30 gcc_4:9.2.1-3.1 gcc-10-base_10-20200222-1 gcc-8-base_8.3.0-29 gcc-9_9.2.1-30 gcc-9-base_9.2.1-30 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3+b1 hostname_3.23 icu-devtools_63.2-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_10-20200222-1 lib32gcc1_1:10-20200222-1 lib32stdc++6_10-20200222-1 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-30 libatomic1_10-20200222-1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.34-3 libblkid1_2.34-0.1 libboost-filesystem-dev_1.67.0.2+b1 libboost-filesystem1.67-dev_1.67.0-17 libboost-filesystem1.67.0_1.67.0-17 libboost-iostreams-dev_1.67.0.2+b1 libboost-iostreams1.67-dev_1.67.0-17 libboost-iostreams1.67.0_1.67.0-17 libboost-program-options-dev_1.67.0.2+b1 libboost-program-options1.67-dev_1.67.0-17 libboost-program-options1.67.0_1.67.0-17 libboost-regex1.67-dev_1.67.0-17 libboost-regex1.67.0_1.67.0-17 libboost-system1.67-dev_1.67.0-17 libboost-system1.67.0_1.67.0-17 libboost1.67-dev_1.67.0-17 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-10 libc-dev-bin_2.29-10 libc6_2.29-10 libc6-dev_2.29-10 libc6-i386_2.29-10 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10-20200222-1 libclang-common-8-dev_1:8.0.1-7 libclang1-8_1:8.0.1-7 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10 libcrypt1_1:4.4.10-10 libctf-nobfd0_2.34-3 libctf0_2.34-3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.9 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgc1c2_1:7.6.4-0.4 libgcc-8-dev_8.3.0-29 libgcc-9-dev_9.2.1-30 libgcc-s1_10-20200222-1 libgcc1_1:10-20200222-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgenome-dev_1.3.11+svn20110227.4616-2 libgenome0_1.3.11+svn20110227.4616-2 libglib2.0-0_2.62.4-2 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.12-2 libgomp1_10-20200222-1 libgpg-error0_1.37-1 libhogweed5_3.5.1+really3.5.1-2 libicu-dev_63.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22.1-1 libitm1_10-20200222-1 libllvm8_1:8.0.1-7 liblsan0_10-20200222-1 liblz4-1_1.9.2-2 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 libmpfr6_4.0.2-1 libmpx2_8.3.0-29 libmuscle-dev_3.7+4565-6 libmuscle1_3.7+4565-6 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libobjc-8-dev_8.3.0-29 libobjc-9-dev_9.2.1-30 libobjc4_10-20200222-1 libomp-8-dev_1:8.0.1-7 libomp5-8_1:8.0.1-7 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_5.30.0-9 libpipeline1_1.5.2-2 libquadmath0_10-20200222-1 libseccomp2_2.4.2-2 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libss2_1.45.5-2 libstdc++-8-dev_8.3.0-29 libstdc++-9-dev_9.2.1-30 libstdc++6_10-20200222-1 libsub-override-perl_0.09-2 libsystemd0_244.3-1 libtasn1-6_4.16.0-2 libtinfo6_6.1+20191019-1 libtool_2.4.6-13 libtsan0_10-20200222-1 libubsan1_10-20200222-1 libuchardet0_0.0.6-3 libudev1_244.3-1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-3 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.19-1 login_1:4.8.1-1 logsave_1.45.5-2 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-2 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pkg-config_0.29-6 po-debconf_1.0.21 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: libmems Binary: libmems-dev, libmems1 Architecture: any Version: 1.6.0+4725-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/libmems Vcs-Git: https://salsa.debian.org/med-team/libmems.git Build-Depends: debhelper (>= 11~), d-shlibs, pkg-config, libgenome-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-dev Package-List: libmems-dev deb libdevel optional arch=any libmems1 deb libs optional arch=any Checksums-Sha1: 717cab0cd606be4ebdb1b5990ee89a85d8d6c39b 236796 libmems_1.6.0+4725.orig.tar.xz 61694e63abfd068b08762e5ab5f5ead4fb8e96bd 8696 libmems_1.6.0+4725-8.debian.tar.xz Checksums-Sha256: 67265e1eb1b85a04533be431b906cc8d4773c799fb1a7809b346209380c41e91 236796 libmems_1.6.0+4725.orig.tar.xz a5877395d9cd6ec389895cbf39b5aa3c8a688b943b1f62aabf04ef9c576dab21 8696 libmems_1.6.0+4725-8.debian.tar.xz Files: a3f12384cfcf888f01b39f562024d5e8 236796 libmems_1.6.0+4725.orig.tar.xz 055e67cca13777db163288075def9d1e 8696 libmems_1.6.0+4725-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAluEVlIRHHRpbGxlQGRl 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F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libmems_1.6.0+4725-8.dsc dpkg-source: info: extracting libmems in /<> dpkg-source: info: unpacking libmems_1.6.0+4725.orig.tar.xz dpkg-source: info: unpacking libmems_1.6.0+4725-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_fix_ctors.patch dpkg-source: info: applying 02_fix_a_Wformat.patch dpkg-source: info: applying pkg-config-directive.patch dpkg-source: info: applying 03_update_boost_m4_to_git_d9ff75.patch dpkg-source: info: applying 04_add_dependend_libs_to_link_command.patch dpkg-source: info: applying 05_gcc-6.patch dpkg-source: info: applying boost1.62.patch dpkg-source: info: applying drop-version-number.patch 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-ef459e55-f0c9-4d15-b1b8-f1db17e7a577 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 libmems dpkg-buildpackage: info: source version 1.6.0+4725-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/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:54: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see: configure.ac:54: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation configure.ac:66: installing 'config/compile' configure.ac:66: installing 'config/config.guess' configure.ac:66: installing 'config/config.sub' configure.ac:54: installing 'config/install-sh' configure.ac:54: installing 'config/missing' libMems/Makefile.am:48: warning: source file 'HomologyHMM/algebras.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. libMems/Makefile.am:48: warning: source file 'HomologyHMM/homology.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled libMems/Makefile.am:48: warning: source file 'HomologyHMM/homologymain.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/asyncio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/alinuxaio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/aPOSIXaio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/alibc.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/awin32aio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/buffer.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/util.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/sorting.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/dmsort.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/timing.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/sml.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am: installing 'config/depcomp' dh_auto_configure ./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 --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode 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 for g++... g++ 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 g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking whether ln -s works... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc 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 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 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 special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for ANSI C header files... (cached) yes checking for Boost headers version >= 1.34.0... yes checking for Boost's header version... 1_67 checking whether the compiler implements namespaces... yes checking for the toolset name used by Boost for g++... gcc42 -gcc checking boost/system/error_code.hpp usability... yes checking boost/system/error_code.hpp presence... yes checking for boost/system/error_code.hpp... yes checking for the Boost system library... yes checking boost/filesystem/path.hpp usability... yes checking boost/filesystem/path.hpp presence... yes checking for boost/filesystem/path.hpp... yes checking for the Boost filesystem library... (cached) yes checking boost/program_options.hpp usability... yes checking boost/program_options.hpp presence... yes checking for boost/program_options.hpp... yes checking for the Boost program_options library... (cached) yes checking boost/iostreams/device/file_descriptor.hpp usability... yes checking boost/iostreams/device/file_descriptor.hpp presence... yes checking for boost/iostreams/device/file_descriptor.hpp... yes checking for the Boost iostreams library... (cached) yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for DEPS... yes checking for sys/types.h... (cached) yes checking sys/aio.h usability... no checking sys/aio.h presence... no checking for sys/aio.h... no checking aio.h usability... yes checking aio.h presence... yes checking for aio.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking for pthread_mutex_unlock in -lpthread... yes checking for aio_write in -lrt... yes checking for doxygen... no configure: WARNING: doxygen not found - will not generate any doxygen documentation checking for perl... /usr/bin/perl checking for an ANSI C-conforming const... yes checking for inline... inline checking whether time.h and sys/time.h may both be included... yes checking whether gcc needs -traditional... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating libMems/Makefile config.status: creating libMems.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_build make -j4 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in libMems make[3]: Entering directory '/<>/libMems' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAFileSML.lo DNAFileSML.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchFinder.lo MatchFinder.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAMemorySML.lo DNAMemorySML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -fPIC -DPIC -o .libs/DNAFileSML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemorySML.lo MemorySML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -o MemorySML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -fPIC -DPIC -o .libs/SortedMerList.o /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileSML.lo FileSML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemHash.lo MemHash.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o In file included from FileSML.cpp:12: In file included from ../libMems/Aligner.h:21: In file included from ../libMems/IntervalList.h:24: ../libMems/CompactGappedAlignment.h:811:6: error: 'swap, std::allocator > > > >' is missing exception specification 'noexcept(__and_, allocator > > > >, is_nothrow_move_assignable, allocator > > > > >::value)' void swap( mems::CompactGappedAlignment<>& a, mems::CompactGappedAlignment<>& b ) ^ noexcept(__and_, allocator > > > >, is_nothrow_move_assignable, allocator > > > > >::value) ../libMems/CompactGappedAlignment.h:811:6: note: previous declaration is here FileSML.cpp:407:31: warning: adding 'mems::smlSeqI_t' (aka 'unsigned int') to a string does not append to the string [-Wstring-plus-int] errmsg += tmp_mer.position + " is out of range\n"; ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ FileSML.cpp:407:31: note: use array indexing to silence this warning /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchHashEntry.lo MatchHashEntry.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o 1 warning and 1 error generated. make[3]: *** [Makefile:792: FileSML.lo] Error 1 make[3]: *** Waiting for unfinished jobs.... libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -o MemHash.o >/dev/null 2>&1 make[3]: Leaving directory '/<>/libMems' make[2]: *** [Makefile:546: all-recursive] Error 1 make[2]: Leaving directory '/<>' make[1]: *** [Makefile:454: all] Error 2 make[1]: Leaving directory '/<>' dh_auto_build: error: make -j4 returned exit code 2 make: *** [debian/rules:6: build] Error 25 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-02-25T14:02:14Z 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: 15408 Build-Time: 53 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 8 Job: libmems_1.6.0+4725-8 Machine Architecture: amd64 Package: libmems Package-Time: 78 Source-Version: 1.6.0+4725-8 Space: 15408 Status: attempted Version: 1.6.0+4725-8 -------------------------------------------------------------------------------- Finished at 2020-02-25T14:02:14Z Build needed 00:01:18, 15408k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 79.718363181s DC-Time-Estimation: 79.718363181 versus expected 435 (r/m: 4.456710131043904 ; m: 79.718363181)