https://launchpad.net/ubuntu/+archive/test-rebuild-20220617-kinetic/+build/23988263 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-044 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_215~563~ubuntu20.04.1 python3-lpbuildd_215~563~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.4 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 23 Jun 23:42:10 ntpdate[1857]: adjust time server 10.211.37.1 offset -0.000652 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23988263 --image-type chroot /home/buildd/filecache-default/4d18961cd05542d5def75b14497015b674c37821 Creating target for build PACKAGEBUILD-23988263 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23988263 Starting target for build PACKAGEBUILD-23988263 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23988263 'deb http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic main' 'deb http://ftpmaster.internal/ubuntu kinetic main universe' Overriding sources.list in build-PACKAGEBUILD-23988263 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23988263 Adding trusted keys to build-PACKAGEBUILD-23988263 pub rsa1024/1E9377A2BA9EF27F 2009-10-22 [SC] Key fingerprint = 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid Launchpad Toolchain builds RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23988263 Updating target for build PACKAGEBUILD-23988263 Get:1 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:2 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic InRelease [23.8 kB] Get:3 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 Packages [9632 B] Get:4 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main Translation-en [4132 B] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 Packages [1398 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe amd64 Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5730 kB] Fetched 22.3 MB in 6s (3534 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libgprofng0 util-linux-extra The following packages will be upgraded: adduser apt base-files binutils binutils-common binutils-x86-64-linux-gnu bsdutils cpp-11 dash dpkg dpkg-dev e2fsprogs fakeroot g++-11 gcc-11 gcc-11-base gcc-12-base init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libext2fs2 libfakeroot libgcc-11-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libip4tc2 libitm1 libkeyutils1 liblsan0 liblzma5 libmount1 libncurses6 libncursesw6 libpng16-16 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-11-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd pinentry-curses policyrcd-script-zg2 readline-common systemd systemd-sysv util-linux xz-utils 84 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 79.8 MB of archives. After this operation, 5324 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu kinetic/main amd64 base-files amd64 12.2ubuntu1 [62.6 kB] Get:2 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf0 amd64 2.38.50.20220615-4ubuntu1 [103 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdutils amd64 1:2.38-4ubuntu1 [80.7 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [270 kB] Get:5 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf-nobfd0 amd64 2.38.50.20220615-4ubuntu1 [107 kB] Get:6 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-x86-64-linux-gnu amd64 2.38.50.20220615-4ubuntu1 [2476 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 libatomic1 amd64 12.1.0-2ubuntu1 [10.4 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main amd64 libubsan1 amd64 12.1.0-2ubuntu1 [969 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 libquadmath0 amd64 12.1.0-2ubuntu1 [152 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblsan0 amd64 12.1.0-2ubuntu1 [1060 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main amd64 libitm1 amd64 12.1.0-2ubuntu1 [29.5 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgomp1 amd64 12.1.0-2ubuntu1 [125 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-12-base amd64 12.1.0-2ubuntu1 [18.8 kB] Get:14 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libbinutils amd64 2.38.50.20220615-4ubuntu1 [655 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-s1 amd64 12.1.0-2ubuntu1 [54.2 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcc1-0 amd64 12.1.0-2ubuntu1 [46.6 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++6 amd64 12.1.0-2ubuntu1 [679 kB] Get:18 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils amd64 2.38.50.20220615-4ubuntu1 [3292 B] Get:19 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-common amd64 2.38.50.20220615-4ubuntu1 [224 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgpg-error0 amd64 1.45-2 [69.0 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcrypt20 amd64 1.10.1-2ubuntu1 [524 kB] Get:22 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libgprofng0 amd64 2.38.50.20220615-4ubuntu1 [963 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblzma5 amd64 5.2.5-2.1 [99.2 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd-sysv amd64 249.11-0ubuntu4 [10.2 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapparmor1 amd64 3.0.4-2ubuntu3 [38.0 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgnutls30 amd64 3.7.6-2ubuntu1 [968 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main amd64 libip4tc2 amd64 1.8.7-1ubuntu6 [19.7 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 libblkid1 amd64 2.38-4ubuntu1 [103 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main amd64 libselinux1 amd64 3.4-1 [77.6 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmount1 amd64 2.38-4ubuntu1 [121 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsmartcols1 amd64 2.38-4ubuntu1 [50.8 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main amd64 login amd64 1:4.11.1+dfsg1-2ubuntu1 [183 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux-extra amd64 2.38-4ubuntu1 [83.8 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux amd64 2.38-4ubuntu1 [1069 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 mount amd64 2.38-4ubuntu1 [114 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage-common all 3.4-1 [9828 B] Get:37 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsepol2 amd64 3.4-2 [294 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage2 amd64 3.4-1 [91.8 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main amd64 passwd amd64 1:4.11.1+dfsg1-2ubuntu1 [765 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main amd64 adduser all 3.121ubuntu1 [150 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd amd64 249.11-0ubuntu4 [4517 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsystemd0 amd64 249.11-0ubuntu4 [314 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 libudev1 amd64 249.11-0ubuntu4 [76.1 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapt-pkg6.0 amd64 2.5.0 [896 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg amd64 1.21.8ubuntu1 [1333 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 dash amd64 0.5.11+git20210903+057cd650a4ed-8ubuntu1 [88.2 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-bin amd64 6.3+20220423-2 [183 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 init-system-helpers all 1.63 [38.7 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main amd64 apt amd64 2.5.0 [1370 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 logsave amd64 1.46.5-2ubuntu2 [9914 B] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 libext2fs2 amd64 1.46.5-2ubuntu2 [205 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 e2fsprogs amd64 1.46.5-2ubuntu2 [585 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 init amd64 1.63 [5674 B] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcap-ng0 amd64 0.8.3-1 [15.7 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.9 [717 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncurses6 amd64 6.3+20220423-2 [110 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncursesw6 amd64 6.3+20220423-2 [146 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/main amd64 libtinfo6 amd64 6.3+20220423-2 [99.6 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic/main amd64 libuuid1 amd64 2.38-4ubuntu1 [23.2 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcom-err2 amd64 1.46.5-2ubuntu2 [9074 B] Get:62 http://ftpmaster.internal/ubuntu kinetic/main amd64 libss2 amd64 1.46.5-2ubuntu2 [12.3 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic/main amd64 mawk amd64 1.3.4.20200120-3.1 [109 kB] Get:64 http://ftpmaster.internal/ubuntu kinetic/main amd64 libkeyutils1 amd64 1.6.1-3ubuntu1 [10.1 kB] Get:65 http://ftpmaster.internal/ubuntu kinetic/main amd64 readline-common all 8.1.2-1.2 [53.6 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic/main amd64 libreadline8 amd64 8.1.2-1.2 [153 kB] Get:67 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsqlite3-0 amd64 3.38.5-1 [646 kB] Get:68 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http://ftpmaster.internal/ubuntu kinetic/main amd64 cpp-11 amd64 11.3.0-3ubuntu1 [9910 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-11-base amd64 11.3.0-3ubuntu1 [20.8 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg-dev all 1.21.8ubuntu1 [1069 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdpkg-perl all 1.21.8ubuntu1 [237 kB] Get:82 http://ftpmaster.internal/ubuntu kinetic/main amd64 lto-disabled-list all 27 [12.4 kB] Get:83 http://ftpmaster.internal/ubuntu kinetic/main amd64 libfakeroot amd64 1.29-1ubuntu1 [31.1 kB] Get:84 http://ftpmaster.internal/ubuntu kinetic/main amd64 fakeroot amd64 1.29-1ubuntu1 [60.0 kB] Get:85 http://ftpmaster.internal/ubuntu kinetic/main amd64 pinentry-curses amd64 1.2.0-1ubuntu1 [34.5 kB] Get:86 http://ftpmaster.internal/ubuntu kinetic/main amd64 policyrcd-script-zg2 all 0.1-3.1 [5730 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 79.8 MB in 6s (13.1 MB/s) 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Setting up libstdc++-11-dev:amd64 (11.3.0-3ubuntu1) ... Setting up gcc-11 (11.3.0-3ubuntu1) ... Setting up g++-11 (11.3.0-3ubuntu1) ... Processing triggers for debianutils (5.7-0.2) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23988263 amd64 kinetic -c chroot:build-PACKAGEBUILD-23988263 --arch=amd64 --dist=kinetic --nolog -A discosnp_2.6.2-1.dsc Initiating build PACKAGEBUILD-23988263 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lgw01-amd64-044.buildd +==============================================================================+ | discosnp 1:2.6.2-1 (amd64) Thu, 23 Jun 2022 23:43:29 +0000 | +==============================================================================+ Package: discosnp Version: 1:2.6.2-1 Source Version: 1:2.6.2-1 Distribution: kinetic Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23988263/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/discosnp-PFUjVE/resolver-bQNtV1' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- discosnp_2.6.2-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/discosnp-PFUjVE/discosnp-2.6.2' with '<>' I: NOTICE: Log filtering will replace 'build/discosnp-PFUjVE' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3, cmake, libgatbcore-dev, libboost-dev, libhdf5-dev, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, cmake, libgatbcore-dev, libboost-dev, libhdf5-dev, zlib1g-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 [410 B] Get:5 copy:/<>/apt_archive ./ Packages [493 B] Fetched 1860 B in 0s (54.4 kB/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 bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-elpa-helper dh-python dh-strip-nondeterminism dwz emacsen-common file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libboost-dev libboost1.74-dev libbrotli1 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgatbcore-dev libgatbcore3 libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu71 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp25 libldap-2.5-0 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libuv1 libxml2 m4 man-db media-types po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.10 python3.10-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build cmake-format dh-make flit python3-build python3-tomli python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config libhdf5-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.10-venv python3.10-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-elpa-helper dh-python dh-strip-nondeterminism dwz emacsen-common file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libboost-dev libboost1.74-dev libbrotli1 libcurl4 libcurl4-openssl-dev libdebhelper-perl libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgatbcore-dev libgatbcore3 libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu71 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp25 libldap-2.5-0 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libuv1 libxml2 m4 man-db media-types po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.10 python3.10-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded. 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libgfortran5 amd64 12.1.0-2ubuntu1 [875 kB] Get:72 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libsz2 amd64 1.0.6-1 [5354 B] Get:73 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhdf5-103-1 amd64 1.10.7+repack-4ubuntu2 [1295 kB] Get:74 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhdf5-cpp-103-1 amd64 1.10.7+repack-4ubuntu2 [129 kB] Get:75 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhdf5-fortran-102 amd64 1.10.7+repack-4ubuntu2 [90.9 kB] Get:76 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhdf5-hl-100 amd64 1.10.7+repack-4ubuntu2 [59.1 kB] Get:77 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhdf5-hl-fortran-100 amd64 1.10.7+repack-4ubuntu2 [33.8 kB] Get:78 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhdf5-hl-cpp-100 amd64 1.10.7+repack-4ubuntu2 [10.6 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu9 [164 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjpeg-turbo8 amd64 2.1.2-0ubuntu1 [134 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjpeg-turbo8-dev amd64 2.1.2-0ubuntu1 [257 kB] Get:82 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjpeg8 amd64 8c-2ubuntu10 [2264 B] Get:83 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjpeg8-dev amd64 8c-2ubuntu10 [1476 B] Get:84 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjpeg-dev amd64 8c-2ubuntu10 [1472 B] Get:85 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libaec-dev amd64 1.0.6-1 [17.9 kB] Get:86 http://ftpmaster.internal/ubuntu kinetic/main amd64 libssl-dev amd64 3.0.3-5ubuntu3 [2372 kB] Get:87 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhdf5-dev amd64 1.10.7+repack-4ubuntu2 [2684 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 57.6 MB in 3s (16.5 MB/s) Selecting previously unselected package libpython3.10-minimal:amd64. (Reading database ... 13498 files and directories currently installed.) Preparing to unpack .../libpython3.10-minimal_3.10.5-1_amd64.deb ... Unpacking libpython3.10-minimal:amd64 (3.10.5-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.4.8-1_amd64.deb ... Unpacking libexpat1:amd64 (2.4.8-1) ... Selecting previously unselected package python3.10-minimal. Preparing to unpack .../python3.10-minimal_3.10.5-1_amd64.deb ... Unpacking python3.10-minimal (3.10.5-1) ... Setting up libpython3.10-minimal:amd64 (3.10.5-1) ... Setting up libexpat1:amd64 (2.4.8-1) ... Setting up python3.10-minimal (3.10.5-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13800 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.10.4-0ubuntu2_amd64.deb ... Unpacking python3-minimal (3.10.4-0ubuntu2) ... Selecting previously unselected package media-types. 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Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.7.1ubuntu1) ... Setting up libbrotli1:amd64 (1.0.9-2build6) ... Setting up libnghttp2-14:amd64 (1.47.0-1) ... Setting up libmagic1:amd64 (1:5.41-4) ... Setting up gettext-base (0.21-6) ... Setting up file (1:5.41-4) ... Setting up libaec0:amd64 (1.0.6-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-6ubuntu1) ... Setting up autotools-dev (20220109.1) ... Setting up libuv1:amd64 (1.44.1-2) ... Setting up emacsen-common (3.0.4) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up dh-elpa-helper (2.0.9ubuntu1) ... Setting up libsigsegv2:amd64 (2.13-1ubuntu3) ... Setting up libssl-dev:amd64 (3.0.3-5ubuntu3) ... Setting up autopoint (0.21-6) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up libjpeg-turbo8:amd64 (2.1.2-0ubuntu1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-6ubuntu1) ... Setting up libssh-4:amd64 (0.9.6-2build1) ... Setting up libgfortran5:amd64 (12.1.0-2ubuntu1) ... Setting up libgatbcore3:amd64 (1.4.2+dfsg-8) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu9) ... Setting up librhash0:amd64 (1.4.2-1ubuntu1) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libmpdec3:amd64 (2.5.1-2build2) ... Setting up libsub-override-perl (0.09-3) ... Setting up cmake-data (3.23.2-1ubuntu1) ... Setting up libboost-dev:amd64 (1.74.0.3ubuntu7) ... Setting up libelf1:amd64 (0.187-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1) ... Setting up libsz2:amd64 (1.0.6-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu10) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:amd64 (0.187-1) ... Setting up libjpeg-turbo8-dev:amd64 (2.1.2-0ubuntu1) ... Setting up gettext (0.21-6) ... Setting up libtool (2.4.7-4) ... Setting up libarchive13:amd64 (3.6.0-1ubuntu1) ... Setting up libaec-dev:amd64 (1.0.6-1) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up libldap-2.5-0:amd64 (2.5.12+dfsg-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython3.10-stdlib:amd64 (3.10.5-1) ... Setting up libgatbcore-dev:amd64 (1.4.2+dfsg-8) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up groff-base (1.22.4-8build1) ... Setting up debugedit (1:5.0-4build1) ... Setting up libcurl4:amd64 (7.83.1-2) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu10) ... Setting up libpython3-stdlib:amd64 (3.10.4-0ubuntu2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.10 (3.10.5-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu10) ... Setting up python3 (3.10.4-0ubuntu2) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up dh-autoreconf (20) ... Setting up libcurl4-openssl-dev:amd64 (7.83.1-2) ... Setting up libhdf5-103-1:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.7+repack-4ubuntu2) ... Setting up cmake (3.23.2-1ubuntu1) ... Setting up python3-lib2to3 (3.10.4-0ubuntu2) ... Setting up libhdf5-hl-100:amd64 (1.10.7+repack-4ubuntu2) ... Setting up python3-distutils (3.10.4-0ubuntu2) ... Setting up dh-python (5.20220403) ... Setting up debhelper (13.7.1ubuntu1) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-fortran-102:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.7+repack-4ubuntu2) ... Setting up libhdf5-dev (1.10.7+repack-4ubuntu2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.38.50.20220615-4ubuntu1 dpkg-dev_1.21.8ubuntu1 g++-11_11.3.0-3ubuntu1 gcc-11_11.3.0-3ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-3ubuntu1 libstdc++6_12.1.0-2ubuntu1 linux-libc-dev_5.15.0-27.28 Package versions: adduser_3.121ubuntu1 advancecomp_2.1-2.1ubuntu2 apt_2.5.0 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2ubuntu1 base-passwd_3.5.52build1 bash_5.1-6ubuntu1 binutils_2.38.50.20220615-4ubuntu1 binutils-common_2.38.50.20220615-4ubuntu1 binutils-x86-64-linux-gnu_2.38.50.20220615-4ubuntu1 bsdextrautils_2.38-4ubuntu1 bsdutils_1:2.38-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 cmake_3.23.2-1ubuntu1 cmake-data_3.23.2-1ubuntu1 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.3.0-3ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-8ubuntu1 debconf_1.5.79ubuntu1 debhelper_13.7.1ubuntu1 debianutils_5.7-0.2 debugedit_1:5.0-4build1 dh-autoreconf_20 dh-elpa-helper_2.0.9ubuntu1 dh-python_5.20220403 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu2 dpkg_1.21.8ubuntu1 dpkg-dev_1.21.8ubuntu1 dwz_0.14-1build2 e2fsprogs_1.46.5-2ubuntu2 emacsen-common_3.0.4 fakeroot_1.29-1ubuntu1 file_1:5.41-4 findutils_4.8.0-1ubuntu3 g++_4:11.2.0-1ubuntu1 g++-11_11.3.0-3ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.3.0-3ubuntu1 gcc-11-base_11.3.0-3ubuntu1 gcc-12-base_12.1.0-2ubuntu1 gettext_0.21-6 gettext-base_0.21-6 gpg_2.2.27-3ubuntu2 gpg-agent_2.2.27-3ubuntu2 gpgconf_2.2.27-3ubuntu2 gpgv_2.2.27-3ubuntu2 grep_3.7-1build1 groff-base_1.22.4-8build1 gzip_1.10-4ubuntu4 hdf5-helpers_1.10.7+repack-4ubuntu2 hostname_3.23ubuntu2 init_1.63 init-system-helpers_1.63 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapparmor1_3.0.4-2ubuntu3 libapt-pkg6.0_2.5.0 libarchive-zip-perl_1.68-1 libarchive13_3.6.0-1ubuntu1 libargon2-1_0~20171227-0.3 libasan6_11.3.0-3ubuntu1 libassuan0_2.5.5-3 libatomic1_12.1.0-2ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1build1 libaudit1_1:3.0.7-1build1 libbinutils_2.38.50.20220615-4ubuntu1 libblkid1_2.38-4ubuntu1 libboost-dev_1.74.0.3ubuntu7 libboost1.74-dev_1.74.0-14ubuntu4 libbrotli1_1.0.9-2build6 libbz2-1.0_1.0.8-5build1 libc-bin_2.35-0ubuntu3 libc-dev-bin_2.35-0ubuntu3 libc6_2.35-0ubuntu3 libc6-dev_2.35-0ubuntu3 libcap-ng0_0.8.3-1 libcap2_1:2.44-1build3 libcc1-0_12.1.0-2ubuntu1 libcom-err2_1.46.5-2ubuntu2 libcrypt-dev_1:4.4.27-1 libcrypt1_1:4.4.27-1 libcryptsetup12_2:2.4.3-1ubuntu1 libctf-nobfd0_2.38.50.20220615-4ubuntu1 libctf0_2.38.50.20220615-4ubuntu1 libcurl4_7.83.1-2 libcurl4-openssl-dev_7.83.1-2 libdb5.3_5.3.28+dfsg1-0.9 libdebconfclient0_0.261ubuntu1 libdebhelper-perl_13.7.1ubuntu1 libdevmapper1.02.1_2:1.02.175-2.1ubuntu4 libdpkg-perl_1.21.8ubuntu1 libdw1_0.187-1 libelf1_0.187-1 libexpat1_2.4.8-1 libext2fs2_1.46.5-2ubuntu2 libfakeroot_1.29-1ubuntu1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgatbcore-dev_1.4.2+dfsg-8 libgatbcore3_1.4.2+dfsg-8 libgcc-11-dev_11.3.0-3ubuntu1 libgcc-s1_12.1.0-2ubuntu1 libgcrypt20_1.10.1-2ubuntu1 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran5_12.1.0-2ubuntu1 libgmp10_2:6.2.1+dfsg-3ubuntu1 libgnutls30_3.7.6-2ubuntu1 libgomp1_12.1.0-2ubuntu1 libgpg-error0_1.45-2 libgprofng0_2.38.50.20220615-4ubuntu1 libgssapi-krb5-2_1.19.2-2 libhdf5-103-1_1.10.7+repack-4ubuntu2 libhdf5-cpp-103-1_1.10.7+repack-4ubuntu2 libhdf5-dev_1.10.7+repack-4ubuntu2 libhdf5-fortran-102_1.10.7+repack-4ubuntu2 libhdf5-hl-100_1.10.7+repack-4ubuntu2 libhdf5-hl-cpp-100_1.10.7+repack-4ubuntu2 libhdf5-hl-fortran-100_1.10.7+repack-4ubuntu2 libhogweed6_3.7.3-1build2 libicu71_71.1-3 libidn2-0_2.3.2-2build1 libip4tc2_1.8.7-1ubuntu6 libisl23_0.24-2build1 libitm1_12.1.0-2ubuntu1 libjpeg-dev_8c-2ubuntu10 libjpeg-turbo8_2.1.2-0ubuntu1 libjpeg-turbo8-dev_2.1.2-0ubuntu1 libjpeg8_8c-2ubuntu10 libjpeg8-dev_8c-2ubuntu10 libjson-c5_0.16-1 libjsoncpp25_1.9.5-4 libk5crypto3_1.19.2-2 libkeyutils1_1.6.1-3ubuntu1 libkmod2_29-1ubuntu1 libkrb5-3_1.19.2-2 libkrb5support0_1.19.2-2 libldap-2.5-0_2.5.12+dfsg-2ubuntu1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_12.1.0-2ubuntu1 liblz4-1_1.9.3-2build2 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38-4ubuntu1 libmpc3_1.2.1-2build1 libmpdec3_2.5.1-2build2 libmpfr6_4.1.0-3build3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 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perl-modules-5.34_5.34.0-3ubuntu1 pinentry-curses_1.2.0-1ubuntu1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-6ubuntu2 python3_3.10.4-0ubuntu2 python3-distutils_3.10.4-0ubuntu2 python3-lib2to3_3.10.4-0ubuntu2 python3-minimal_3.10.4-0ubuntu2 python3.10_3.10.5-1 python3.10-minimal_3.10.5-1 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 systemd_249.11-0ubuntu4 systemd-sysv_249.11-0ubuntu4 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build3 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-2ubuntu9 zlib1g-dev_1:1.2.11.dfsg-2ubuntu9 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: discosnp Binary: discosnp Architecture: any Version: 1:2.6.2-1 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Andreas Tille Homepage: http://colibread.inria.fr/discosnp/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/discosnp Vcs-Git: https://salsa.debian.org/med-team/discosnp.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: debhelper-compat (= 13), dh-python, python3, cmake, libgatbcore-dev, libboost-dev, libhdf5-dev, zlib1g-dev Package-List: discosnp deb science optional arch=any Checksums-Sha1: 8658a569f07cf68056126a75398759d83ad7c5f0 1390275 discosnp_2.6.2.orig.tar.gz 4f6a60f047a6d1ed647152e51f90224f2665be0a 22256 discosnp_2.6.2-1.debian.tar.xz Checksums-Sha256: 06c3683b2aaa665daf43254b4d97a7d0516dcea1c551a72e17669f2d52ad1fd6 1390275 discosnp_2.6.2.orig.tar.gz fd38bd2d941064a79d1268e0267487342e6c2932190c71d550e86b10bbc18562 22256 discosnp_2.6.2-1.debian.tar.xz Files: e6e7099629b69ead20a34f61e881aeb3 1390275 discosnp_2.6.2.orig.tar.gz bc24d5a59ae6bd0b44a47383a5574172 22256 discosnp_2.6.2-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmIOdckRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF+wA//VXhXm3ksGCvIvlHVQISOo2a0Dyr/5LAf RNxWnRwEPZFUUP2dRXo/zpRcYhIot1AKHjKLBDXCYzbUK80HFn/L/7fwh3wakHL2 8/hbgxXUWl3tEiVepvdrDePrur33hAtb3OPtPV2d7ldscwqVleWOWwXG4kui0X+V uRn058SmbVMsLhfmgWhgfNc1muGe1/tIIFv3eAPdlqZisXYBrb4W/TWu+e+vYBoi mOZIT7d4i3ArrgneKIgVuWli4fZqWstStIQYIcCZqPc7yOhABC6+91wVDI4e9gQG B727oa5SqWJWOSkLxhMwxZk+yD3KRBdGPiJQs1Lsbb48JMMQPr1oiPuWhQktheOT APIgeZbnS7DfmO+GF8ylWRUTSz6mVoTj2a33DJNm7RJ8z/wC4Vw7fxZp4B8Vua2X FWxi77YG0viXLY9lgx7vEvWPG/w3Mh8Z7r1R4jZ+CDD7VXI2FxWzmavg2XtmHObL ceyfyjKb9CcN5DXOkEIdvUdiQhz+Egi9PDRhAddAmqbBVHUMGEwaxl4GJ4hRP9n8 f90sRHlkxlC+Vhj7RUn8Q/TCFjEiGNwH4nOoduysqC5UmpkFSyezap5dpNdw8WdO tDhD6hfZt+8lwgsuvq+L8cZrhV9z2++V93jZWejRdwvWZb6Ay4LozK90M3MR6kH3 8aj4AMMWizI= =IyBW -----END PGP SIGNATURE----- gpgv: Signature made Thu Feb 17 16:20:25 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./discosnp_2.6.2-1.dsc dpkg-source: info: extracting discosnp in /<> dpkg-source: info: unpacking discosnp_2.6.2.orig.tar.gz dpkg-source: info: unpacking discosnp_2.6.2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_gatb-core.patch dpkg-source: info: applying no_install_to_wrong_dir.patch dpkg-source: info: applying path_to_readme_file_names.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying adapt_test_scripts.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying shell_syntax.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-23988263 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23988263 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23988263 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package discosnp dpkg-buildpackage: info: source version 1:2.6.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY -- Build files have been written to: /<>/obj-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/kissnp2 /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/kissnp2 /<>/obj-x86_64-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake --color= make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/depend make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/kissreads2 /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/kissreads2 /<>/obj-x86_64-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/DependInfo.cmake --color= make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/QHC /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/QHC /<>/obj-x86_64-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake --color= make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/read_file_names /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/read_file_names /<>/obj-x86_64-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/<>/tools/kissnp2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -MF CMakeFiles/kissnp2.dir/src/Bubble.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -c /<>/tools/kissnp2/src/Bubble.cpp make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/build make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 10%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/QHC && /usr/bin/c++ -I/<>/tools/QHC/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -MF CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o.d -o CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -c /<>/tools/QHC/src/quick_hierarchical_clustering.cpp [ 15%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/<>/tools/kissreads2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -MF CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o.d -o CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -c /<>/tools/kissreads2/src/Kissreads2.cpp [ 20%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/read_file_names && /usr/bin/c++ -I/<>/tools/read_file_names/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -MF CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o.d -o CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -c /<>/tools/read_file_names/src/get_read_file_names.cpp [ 25%] Linking CXX executable ../../bin/quick_hierarchical_clustering cd /<>/obj-x86_64-linux-gnu/tools/QHC && /usr/bin/cmake -E cmake_link_script CMakeFiles/quick_hierarchical_clustering.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -rdynamic CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -o ../../bin/quick_hierarchical_clustering -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 25%] Built target quick_hierarchical_clustering make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' cd /<>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tools/create_coverage_h5_file /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/tools/create_coverage_h5_file /<>/obj-x86_64-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 30%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/create_coverage_h5_file && /usr/bin/c++ -I/<>/tools/create_coverage_h5_file/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -MF CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o.d -o CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -c /<>/tools/create_coverage_h5_file/src/create_coverage_h5_file.cpp [ 35%] Linking CXX executable ../../bin/read_file_names cd /<>/obj-x86_64-linux-gnu/tools/read_file_names && /usr/bin/cmake -E cmake_link_script CMakeFiles/read_file_names.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -rdynamic CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -o ../../bin/read_file_names -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 35%] Built target read_file_names [ 40%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/<>/tools/kissnp2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o -MF CMakeFiles/kissnp2.dir/src/Filter.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Filter.cpp.o -c /<>/tools/kissnp2/src/Filter.cpp [ 45%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/<>/tools/kissnp2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -MF CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o.d -o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -c /<>/tools/kissnp2/src/Kissnp2.cpp [ 50%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/<>/tools/kissreads2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o -MF CMakeFiles/kissreads2.dir/src/commons.cpp.o.d -o CMakeFiles/kissreads2.dir/src/commons.cpp.o -c /<>/tools/kissreads2/src/commons.cpp [ 55%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/<>/tools/kissnp2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o -MF CMakeFiles/kissnp2.dir/src/main.cpp.o.d -o CMakeFiles/kissnp2.dir/src/main.cpp.o -c /<>/tools/kissnp2/src/main.cpp [ 60%] Linking CXX executable ../../bin/create_coverage_h5_file cd /<>/obj-x86_64-linux-gnu/tools/create_coverage_h5_file && /usr/bin/cmake -E cmake_link_script CMakeFiles/create_coverage_h5_file.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -rdynamic CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -o ../../bin/create_coverage_h5_file -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz [ 65%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/<>/tools/kissreads2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment.cpp.o -MF CMakeFiles/kissreads2.dir/src/fragment.cpp.o.d -o CMakeFiles/kissreads2.dir/src/fragment.cpp.o -c /<>/tools/kissreads2/src/fragment.cpp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 65%] Built target create_coverage_h5_file [ 70%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/<>/tools/kissreads2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -MF CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o.d -o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -c /<>/tools/kissreads2/src/fragment_index.cpp [ 75%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/<>/tools/kissreads2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o -MF CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o.d -o CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o -c /<>/tools/kissreads2/src/interface_xhash.cpp [ 80%] Linking CXX executable ../../bin/kissnp2 cd /<>/obj-x86_64-linux-gnu/tools/kissnp2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -rdynamic CMakeFiles/kissnp2.dir/src/Bubble.cpp.o CMakeFiles/kissnp2.dir/src/Filter.cpp.o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz [ 85%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/<>/tools/kissreads2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o -MF CMakeFiles/kissreads2.dir/src/main.cpp.o.d -o CMakeFiles/kissreads2.dir/src/main.cpp.o -c /<>/tools/kissreads2/src/main.cpp make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [ 90%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/<>/tools/kissreads2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o -MF CMakeFiles/kissreads2.dir/src/outputs.cpp.o.d -o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -c /<>/tools/kissreads2/src/outputs.cpp [ 90%] Built target kissnp2 [ 95%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o cd /<>/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/<>/tools/kissreads2/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT tools/kissreads2/CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o -MF CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o.d -o CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o -c /<>/tools/kissreads2/src/read_mapper.cpp [100%] Linking CXX executable ../../bin/kissreads2 cd /<>/obj-x86_64-linux-gnu/tools/kissreads2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissreads2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -rdynamic CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o CMakeFiles/kissreads2.dir/src/commons.cpp.o CMakeFiles/kissreads2.dir/src/fragment.cpp.o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o CMakeFiles/kissreads2.dir/src/interface_xhash.cpp.o CMakeFiles/kissreads2.dir/src/main.cpp.o CMakeFiles/kissreads2.dir/src/outputs.cpp.o CMakeFiles/kissreads2.dir/src/read_mapper.cpp.o -o ../../bin/kissreads2 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' [100%] Built target kissreads2 make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/discosnp/ cd obj-x86_64-linux-gnu && make -j4 install DESTDIR=/<>/debian/discosnp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/discosnp/usr/bin/kissnp2 -- Set runtime path of "/<>/debian/discosnp/usr/bin/kissnp2" to "" -- Installing: /<>/debian/discosnp/usr/bin/kissreads2 -- Set runtime path of "/<>/debian/discosnp/usr/bin/kissreads2" to "" -- Installing: /<>/debian/discosnp/usr/bin/quick_hierarchical_clustering -- Set runtime path of "/<>/debian/discosnp/usr/bin/quick_hierarchical_clustering" to "" -- Installing: /<>/debian/discosnp/usr/bin/read_file_names -- Set runtime path of "/<>/debian/discosnp/usr/bin/read_file_names" to "" -- Installing: /<>/debian/discosnp/usr/bin/create_coverage_h5_file -- Set runtime path of "/<>/debian/discosnp/usr/bin/create_coverage_h5_file" to "" make[1]: Leaving directory '/<>/obj-x86_64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install mkdir -p debian/discosnp/usr/lib/discosnp/bin mv debian/discosnp/usr/bin/read_file_names debian/discosnp/usr/lib/discosnp/bin mv debian/discosnp/usr/bin/quick_hierarchical_clustering debian/discosnp/usr/lib/discosnp/bin rm -rf debian/discosnp/usr/share/discosnp/scripts/jenkins make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman # dh_installman interprets .sh as language - just copy manpages manually cp -a debian/mans/*.sh.1 debian/discosnp/usr/share/man/man1 make[1]: Leaving directory '/<>' dh_python3 I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/create_filtered_vcf.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/vcf_formatting_functions.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_common.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_facts_to_gfa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_filter_badly_overlapping_variants.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_node_ids_to_node_sequences.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_paths_to_fa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_phased_paths_to_fa.py dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a debugedit: debian/discosnp/usr/bin/kissreads2: Unknown DWARF DW_FORM_0x1f20 d927d628e9090876c31298ae5a3f6091ecd44e39 debugedit: debian/discosnp/usr/bin/kissnp2: Unknown DWARF DW_FORM_0x1f20 c53494a476f6b184b092da24530bab54a177ddcd debugedit: debian/discosnp/usr/bin/create_coverage_h5_file: Unknown DWARF DW_FORM_0x1f21 d52a89b1f17463761cb2a4ad74eb443ff6a2e69a debugedit: debian/discosnp/usr/lib/discosnp/bin/read_file_names: Unknown DWARF DW_FORM_0x1f20 35910c8ff33ede5f9de543bbdf7321a2edfcf782 debugedit: debian/discosnp/usr/lib/discosnp/bin/quick_hierarchical_clustering: Unknown DWARF DW_FORM_0x1f21 19b312fc6eb5cfffeee298e73bf77f8738d36309 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 149 pkgstriptranslations: processing discosnp (in debian/discosnp); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/discosnp/DEBIAN/control, package discosnp, directory debian/discosnp pkgstripfiles: Truncating usr/share/doc/discosnp/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package discosnp ... pkgstripfiles: No PNG files. dpkg-deb: building package 'discosnp' in '../discosnp_2.6.2-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../discosnp_2.6.2-1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../discosnp_2.6.2-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-06-23T23:49:42Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ discosnp_2.6.2-1_amd64.changes: ------------------------------- Format: 1.8 Date: Thu, 17 Feb 2022 16:58:46 +0100 Source: discosnp Binary: discosnp Built-For-Profiles: noudeb Architecture: amd64 Version: 1:2.6.2-1 Distribution: kinetic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: discosnp - discovering Single Nucleotide Polymorphism from raw set(s) of rea Changes: discosnp (1:2.6.2-1) unstable; urgency=medium . [ Étienne Mollier ] * Adjust use_debian_packaged_gatb-core.patch to not include GatbCore . [ Andreas Tille ] * New upstream version Checksums-Sha1: 3d365dd4c46c5eb9a0c46f53fd91b41442e0cbb0 7851 discosnp_2.6.2-1_amd64.buildinfo 3ff7eb8eaf1b637747ee9d9b47943bdb3a796682 1441772 discosnp_2.6.2-1_amd64.deb Checksums-Sha256: 21426cf9231713b3863a58d60daeb8d80bdfe08c0ccf194cf16b683ff5a3acce 7851 discosnp_2.6.2-1_amd64.buildinfo 857f475bd92d5d22cd9fbc9d46913480571d8fc1d9d34f8749e41a016d4da3ba 1441772 discosnp_2.6.2-1_amd64.deb Files: b441fbf6308df4423d1767f6c96e50ed 7851 science optional discosnp_2.6.2-1_amd64.buildinfo 8602dd2e75c03abd88f3dd933497b10b 1441772 science optional discosnp_2.6.2-1_amd64.deb /<>/discosnp_2.6.2-1_amd64.changes.new could not be renamed to /<>/discosnp_2.6.2-1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: discosnp Binary: discosnp Architecture: amd64 Version: 1:2.6.2-1 Checksums-Md5: 8602dd2e75c03abd88f3dd933497b10b 1441772 discosnp_2.6.2-1_amd64.deb Checksums-Sha1: 3ff7eb8eaf1b637747ee9d9b47943bdb3a796682 1441772 discosnp_2.6.2-1_amd64.deb Checksums-Sha256: 857f475bd92d5d22cd9fbc9d46913480571d8fc1d9d34f8749e41a016d4da3ba 1441772 discosnp_2.6.2-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Thu, 23 Jun 2022 23:49:41 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-6), autotools-dev (= 20220109.1), base-files (= 12.2ubuntu1), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38.50.20220615-4ubuntu1), binutils-common (= 2.38.50.20220615-4ubuntu1), binutils-x86-64-linux-gnu (= 2.38.50.20220615-4ubuntu1), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), cmake (= 3.23.2-1ubuntu1), cmake-data (= 3.23.2-1ubuntu1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-3ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8ubuntu1), debconf (= 1.5.79ubuntu1), debhelper (= 13.7.1ubuntu1), debianutils (= 5.7-0.2), debugedit (= 1:5.0-4build1), dh-autoreconf (= 20), dh-elpa-helper (= 2.0.9ubuntu1), dh-python (= 5.20220403), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), dpkg (= 1.21.8ubuntu1), dpkg-dev (= 1.21.8ubuntu1), dwz (= 0.14-1build2), emacsen-common (= 3.0.4), file (= 1:5.41-4), findutils (= 4.8.0-1ubuntu3), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.3.0-3ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.3.0-3ubuntu1), gcc-11-base (= 11.3.0-3ubuntu1), gcc-12-base (= 12.1.0-2ubuntu1), gettext (= 0.21-6), gettext-base (= 0.21-6), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.10-4ubuntu4), hdf5-helpers (= 1.10.7+repack-4ubuntu2), hostname (= 3.23ubuntu2), init-system-helpers (= 1.63), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libaec-dev (= 1.0.6-1), libaec0 (= 1.0.6-1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.6.0-1ubuntu1), libasan6 (= 11.3.0-3ubuntu1), libatomic1 (= 12.1.0-2ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1build1), libaudit1 (= 1:3.0.7-1build1), libbinutils (= 2.38.50.20220615-4ubuntu1), libblkid1 (= 2.38-4ubuntu1), libboost-dev (= 1.74.0.3ubuntu7), libboost1.74-dev (= 1.74.0-14ubuntu4), libbrotli1 (= 1.0.9-2build6), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.35-0ubuntu3), libc-dev-bin (= 2.35-0ubuntu3), libc6 (= 2.35-0ubuntu3), libc6-dev (= 2.35-0ubuntu3), libcap-ng0 (= 0.8.3-1), libcap2 (= 1:2.44-1build3), libcc1-0 (= 12.1.0-2ubuntu1), libcom-err2 (= 1.46.5-2ubuntu2), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libctf-nobfd0 (= 2.38.50.20220615-4ubuntu1), libctf0 (= 2.38.50.20220615-4ubuntu1), libcurl4 (= 7.83.1-2), libcurl4-openssl-dev (= 7.83.1-2), libdb5.3 (= 5.3.28+dfsg1-0.9), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.7.1ubuntu1), libdpkg-perl (= 1.21.8ubuntu1), libdw1 (= 0.187-1), libelf1 (= 0.187-1), libexpat1 (= 2.4.8-1), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), libgatbcore-dev (= 1.4.2+dfsg-8), libgatbcore3 (= 1.4.2+dfsg-8), libgcc-11-dev (= 11.3.0-3ubuntu1), libgcc-s1 (= 12.1.0-2ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgfortran5 (= 12.1.0-2ubuntu1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgnutls30 (= 3.7.6-2ubuntu1), libgomp1 (= 12.1.0-2ubuntu1), libgpg-error0 (= 1.45-2), libgprofng0 (= 2.38.50.20220615-4ubuntu1), libgssapi-krb5-2 (= 1.19.2-2), libhdf5-103-1 (= 1.10.7+repack-4ubuntu2), libhdf5-cpp-103-1 (= 1.10.7+repack-4ubuntu2), libhdf5-dev (= 1.10.7+repack-4ubuntu2), libhdf5-fortran-102 (= 1.10.7+repack-4ubuntu2), libhdf5-hl-100 (= 1.10.7+repack-4ubuntu2), libhdf5-hl-cpp-100 (= 1.10.7+repack-4ubuntu2), libhdf5-hl-fortran-100 (= 1.10.7+repack-4ubuntu2), libhogweed6 (= 3.7.3-1build2), libicu71 (= 71.1-3), libidn2-0 (= 2.3.2-2build1), libisl23 (= 0.24-2build1), libitm1 (= 12.1.0-2ubuntu1), libjpeg-dev (= 8c-2ubuntu10), libjpeg-turbo8 (= 2.1.2-0ubuntu1), libjpeg-turbo8-dev (= 2.1.2-0ubuntu1), libjpeg8 (= 8c-2ubuntu10), libjpeg8-dev (= 8c-2ubuntu10), libjsoncpp25 (= 1.9.5-4), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-3ubuntu1), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), libldap-2.5-0 (= 2.5.12+dfsg-2ubuntu1), liblsan0 (= 12.1.0-2ubuntu1), liblz4-1 (= 1.9.3-2build2), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpdec3 (= 2.5.1-2build2), libmpfr6 (= 4.1.0-3build3), libncurses6 (= 6.3+20220423-2), libncursesw6 (= 6.3+20220423-2), libnettle8 (= 3.7.3-1build2), libnghttp2-14 (= 1.47.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.24.1-1), libpam-modules (= 1.4.0-13ubuntu1), libpam-modules-bin (= 1.4.0-13ubuntu1), 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python3-minimal (= 3.10.4-0ubuntu2), python3.10 (= 3.10.5-1), python3.10-minimal (= 3.10.5-1), readline-common (= 8.1.2-1.2), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="noautodbgsym parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1645113526" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ discosnp_2.6.2-1_amd64.deb -------------------------- new Debian package, version 2.0. size 1441772 bytes: control archive=4989 bytes. 1238 bytes, 27 lines control 10719 bytes, 118 lines md5sums 301 bytes, 12 lines * postinst #!/bin/sh 407 bytes, 12 lines * prerm #!/bin/sh Package: discosnp Version: 1:2.6.2-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2621 Depends: libc6 (>= 2.34), libgatbcore3 (>= 1.4.2), libgcc-s1 (>= 3.3.1), libhdf5-103-1, libstdc++6 (>= 11), zlib1g (>= 1:1.2.6), python3:any, python3, gatb-core Section: science Priority: optional Homepage: http://colibread.inria.fr/discosnp/ Description: discovering Single Nucleotide Polymorphism from raw set(s) of reads Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS). . Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed. . The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP: . 1) its mean read coverage 2) the (phred) quality of reads generating the polymorphism. . 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drwxr-xr-x root/root 0 2022-02-17 15:58 ./usr/share/python3/runtime.d/ -rwxr-xr-x root/root 137 2022-02-17 15:58 ./usr/share/python3/runtime.d/discosnp.rtupdate +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 83464 Build-Time: 287 Distribution: kinetic Host Architecture: amd64 Install-Time: 81 Job: discosnp_2.6.2-1.dsc Machine Architecture: amd64 Package: discosnp Package-Time: 373 Source-Version: 1:2.6.2-1 Space: 83464 Status: successful Version: 1:2.6.2-1 -------------------------------------------------------------------------------- Finished at 2022-06-23T23:49:42Z Build needed 00:06:13, 83464k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23988263 Scanning for processes to kill in build PACKAGEBUILD-23988263