https://launchpad.net/ubuntu/+archive/test-rebuild-20220617-kinetic/+build/23996433 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-020 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... 22 Jun 12:50:15 ntpdate[1813]: adjust time server 10.211.37.1 offset -0.000340 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23996433 --image-type chroot /home/buildd/filecache-default/4d18961cd05542d5def75b14497015b674c37821 Creating target for build PACKAGEBUILD-23996433 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23996433 Starting target for build PACKAGEBUILD-23996433 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23996433 '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-23996433 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-23996433 Adding trusted keys to build-PACKAGEBUILD-23996433 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-23996433 Updating target for build PACKAGEBUILD-23996433 Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic InRelease [23.8 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic InRelease [267 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 [13.9 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5728 kB] Fetched 21.9 MB in 4s (5871 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 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 83 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 79.7 MB of archives. After this operation, 5304 kB of additional disk space will be used. Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf0 amd64 2.38.50.20220615-4ubuntu1 [103 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic/main amd64 base-files amd64 12.2ubuntu1 [62.6 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdutils amd64 1:2.38-4ubuntu1 [80.7 kB] Get:4 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf-nobfd0 amd64 2.38.50.20220615-4ubuntu1 [107 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [270 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://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-s1 amd64 12.1.0-2ubuntu1 [54.2 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcc1-0 amd64 12.1.0-2ubuntu1 [46.6 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++6 amd64 12.1.0-2ubuntu1 [679 kB] Get:17 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libbinutils amd64 2.38.50.20220615-4ubuntu1 [655 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgpg-error0 amd64 1.45-2 [69.0 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcrypt20 amd64 1.10.1-2ubuntu1 [524 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblzma5 amd64 5.2.5-2.1 [99.2 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd-sysv amd64 249.11-0ubuntu4 [10.2 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapparmor1 amd64 3.0.4-2ubuntu3 [38.0 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgnutls30 amd64 3.7.6-2ubuntu1 [968 kB] Get:24 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils amd64 2.38.50.20220615-4ubuntu1 [3292 B] Get:25 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-common amd64 2.38.50.20220615-4ubuntu1 [224 kB] Get:26 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libgprofng0 amd64 2.38.50.20220615-4ubuntu1 [963 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 ncurses-bin amd64 6.3+20220423-2 [183 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 init-system-helpers all 1.63 [38.7 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 apt amd64 2.5.0 [1370 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main amd64 logsave amd64 1.46.5-2ubuntu2 [9914 B] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 libext2fs2 amd64 1.46.5-2ubuntu2 [205 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 e2fsprogs amd64 1.46.5-2ubuntu2 [585 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 init amd64 1.63 [5674 B] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcap-ng0 amd64 0.7.9-4 [12.1 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.9 [717 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncurses6 amd64 6.3+20220423-2 [110 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncursesw6 amd64 6.3+20220423-2 [146 kB] Get:58 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23996433 amd64 kinetic -c chroot:build-PACKAGEBUILD-23996433 --arch=amd64 --dist=kinetic --nolog -A gemma_0.98.5+dfsg-1build1.dsc Initiating build PACKAGEBUILD-23996433 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-amd64-020.buildd +==============================================================================+ | gemma 0.98.5+dfsg-1build1 (amd64) Wed, 22 Jun 2022 12:50:39 +0000 | +==============================================================================+ Package: gemma Version: 0.98.5+dfsg-1build1 Source Version: 0.98.5+dfsg-1build1 Distribution: kinetic Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23996433/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/gemma-ab8SOm/resolver-geSMWK' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gemma_0.98.5+dfsg-1build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/gemma-ab8SOm/gemma-0.98.5+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/gemma-ab8SOm' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2, ruby, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2, ruby, 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 [425 B] Get:5 copy:/<>/apt_archive ./ Packages [499 B] Fetched 1881 B in 0s (90.3 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 catch debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-11 groff-base intltool-debian libarchive-zip-perl libbsd0 libdebhelper-perl libdw1 libedit2 libeigen3-dev libelf1 libfile-stripnondeterminism-perl libgfortran-11-dev libgfortran5 libglib2.0-0 libgsl-dev libgsl27 libgslcblas0 libicu71 libmagic-mgc libmagic1 libmd0 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libpipeline1 libruby3.0 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db pkg-config po-debconf rake ruby ruby-net-telnet ruby-rubygems ruby-webrick ruby-xmlrpc ruby3.0 rubygems-integration shunit2 zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-11-multilib gfortran-11-doc libcoarrays-dev groff libeigen3-doc libmpfrc++-dev gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl ri ruby-dev bundler Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils catch debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-11 groff-base intltool-debian libarchive-zip-perl libbsd0 libdebhelper-perl libdw1 libedit2 libeigen3-dev libelf1 libfile-stripnondeterminism-perl libgfortran-11-dev libgfortran5 libglib2.0-0 libgsl-dev libgsl27 libgslcblas0 libicu71 libmagic-mgc libmagic1 libmd0 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libpipeline1 libruby3.0 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db pkg-config po-debconf rake ruby ruby-net-telnet ruby-rubygems ruby-webrick ruby-xmlrpc ruby3.0 rubygems-integration sbuild-build-depends-main-dummy shunit2 zlib1g-dev 0 upgraded, 63 newly installed, 0 to remove and 0 not upgraded. Need to get 53.8 MB of archives. After this operation, 263 MB of additional disk space will be used. 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http://ftpmaster.internal/ubuntu kinetic/main amd64 gfortran-11 amd64 11.3.0-3ubuntu1 [11.1 MB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 gfortran amd64 4:11.2.0-1ubuntu1 [1182 B] Get:44 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libgslcblas0 amd64 2.7.1+dfsg-3 [94.4 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libgsl27 amd64 2.7.1+dfsg-3 [1000 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libgsl-dev amd64 2.7.1+dfsg-3 [1257 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libopenblas0-pthread amd64 0.3.20+ds-2 [6774 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libopenblas0 amd64 0.3.20+ds-2 [6076 B] Get:49 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libopenblas-pthread-dev amd64 0.3.20+ds-2 [4625 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libopenblas-dev amd64 0.3.20+ds-2 [18.4 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 rubygems-integration all 1.18 [5336 B] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby3.0 amd64 3.0.2-7ubuntu2 [50.1 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby-rubygems all 3.3.15-1 [231 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby amd64 1:3.0~exp1 [5100 B] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 rake all 13.0.6-3 [61.6 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby-net-telnet all 0.1.1-2.1 [13.1 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby-webrick all 1.7.0-3 [51.8 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main amd64 ruby-xmlrpc all 0.3.2-2 [24.8 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic/main amd64 libruby3.0 amd64 3.0.2-7ubuntu2 [5115 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic/main amd64 pkg-config amd64 0.29.2-1ubuntu3 [48.2 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic/universe amd64 shunit2 all 2.1.6-1.2 [38.5 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu9 [164 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libeigen3-dev all 3.4.0-2ubuntu2 [1056 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.8 MB in 2s (35.0 MB/s) Selecting previously unselected package libmd0:amd64. (Reading database ... 13495 files and directories currently installed.) Preparing to unpack .../00-libmd0_1.0.4-1build1_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-1build1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.11.6-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.6-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../02-libelf1_0.187-1_amd64.deb ... Unpacking libelf1:amd64 (0.187-1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../03-libglib2.0-0_2.72.2-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.72.2-2) ... Selecting previously unselected package libicu71:amd64. Preparing to unpack .../04-libicu71_71.1-3_amd64.deb ... Unpacking libicu71:amd64 (71.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../05-libxml2_2.9.14+dfsg-1_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1) ... 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No schema files found: doing nothing. Setting up libdebhelper-perl (13.7.1ubuntu1) ... Setting up libmagic1:amd64 (1:5.41-4) ... Setting up gettext-base (0.21-6) ... Setting up libgsl27:amd64 (2.7.1+dfsg-3) ... Setting up rubygems-integration (1.18) ... Setting up file (1:5.41-4) ... Setting up autotools-dev (20220109.1) ... Setting up ruby-net-telnet (0.1.1-2.1) ... Setting up libsigsegv2:amd64 (2.13-1ubuntu3) ... Setting up autopoint (0.21-6) ... Setting up pkg-config (0.29.2-1ubuntu3) ... Setting up libgfortran5:amd64 (12.1.0-2ubuntu1) ... Setting up ruby-webrick (1.7.0-3) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu9) ... Setting up libmd0:amd64 (1.0.4-1build1) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up catch (1.12.1-1.1ubuntu1) ... Setting up libsub-override-perl (0.09-3) ... Setting up libbsd0:amd64 (0.11.6-1) ... Setting up libelf1:amd64 (0.187-1) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:amd64 (0.187-1) ... Setting up gettext (0.21-6) ... Setting up libgsl-dev (2.7.1+dfsg-3) ... Setting up libopenblas0-pthread:amd64 (0.3.20+ds-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libtool (2.4.7-4) ... Setting up libgfortran-11-dev:amd64 (11.3.0-3ubuntu1) ... Setting up libedit2:amd64 (3.1-20210910-1build1) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libeigen3-dev (3.4.0-2ubuntu2) ... Setting up gfortran-11 (11.3.0-3ubuntu1) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up libopenblas0:amd64 (0.3.20+ds-2) ... Setting up groff-base (1.22.4-8build1) ... Setting up debugedit (1:5.0-4build1) ... 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 libopenblas-pthread-dev:amd64 (0.3.20+ds-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up po-debconf (1.0.21+nmu1) ... 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 gfortran (4:11.2.0-1ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up dh-autoreconf (20) ... Setting up libopenblas-dev:amd64 (0.3.20+ds-2) ... Setting up debhelper (13.7.1ubuntu1) ... Setting up libruby3.0:amd64 (3.0.2-7ubuntu2) ... Setting up ruby3.0 (3.0.2-7ubuntu2) ... Setting up ruby (1:3.0~exp1) ... Setting up rake (13.0.6-3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up ruby-rubygems (3.3.15-1) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | 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 catch_1.12.1-1.1ubuntu1 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.3.0-3ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3build1 debconf_1.5.79ubuntu1 debhelper_13.7.1ubuntu1 debianutils_5.7-0.2 debugedit_1:5.0-4build1 dh-autoreconf_20 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 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 gfortran_4:11.2.0-1ubuntu1 gfortran-11_11.3.0-3ubuntu1 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gemma Binary: gemma, gemma-doc Architecture: any all Version: 0.98.5+dfsg-1build1 Maintainer: Ubuntu Developers Uploaders: Steffen Moeller Homepage: https://www.xzlab.org/software.html Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/gemma Vcs-Git: https://salsa.debian.org/med-team/gemma.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2, ruby Package-List: gemma deb science optional arch=any gemma-doc deb doc optional arch=all Checksums-Sha1: 362ef505335ef6e1554193290ac7b423c9602494 44173556 gemma_0.98.5+dfsg.orig.tar.xz f9b2aa8c7934f3b6ed6e4621c24aff5283f8c7d8 6700 gemma_0.98.5+dfsg-1build1.debian.tar.xz Checksums-Sha256: 6a9741ad53d2c581d0fb850de5807ca61fb3449f1d198bbab78291487187619a 44173556 gemma_0.98.5+dfsg.orig.tar.xz d3894a35f97dda4fdaa3c239b62db22eb33b94747b697c9ef14232cf35551dda 6700 gemma_0.98.5+dfsg-1build1.debian.tar.xz Files: 7ecee9f8cca7d1d5aff408d27dce7840 44173556 gemma_0.98.5+dfsg.orig.tar.xz 45bcacfa620616f2172da583b86a952c 6700 gemma_0.98.5+dfsg-1build1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQJOBAEBCgA4FiEErEg/aN5yj0PyIC/KVo0w8yGyEz0FAmGvmlIaHHN0ZXZlLmxh bmdhc2VrQHVidW50dS5jb20ACgkQVo0w8yGyEz1WNRAAl+nQlBpWchgKWcaMZdNw zrS+BMVvrDZHPFWwAbatyo/qUeOS1wzwWGqAsRDOSkRqipADEQkLTRI3J4RCCtKZ 1Yw9u8vD1AZTocpa9Wj3Ew6YT6pEmUfSCqnit2nXHq0/mm333G6LsAqYN7iP7AkD MOICN5nicpgujJNFL5REr/idxikAibsF7JCDC+jOFEZe9FX6SzSl9N89wjA1hAKw b4Zi5wRb5yY4lCbLF7QFXssK6Y9X4oU2DHN55voC7JA0uH7b8wGvQL9LNaOBN3/L /MUsK7JHyC3oc2eE8K9ffgdBWm/JwDJw9jvhBnzdP8McDnxGSgr0hC9DSPtB2Yma 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applying Reproducible_builds.patch dpkg-source: info: applying no-lquadmath.patch dpkg-source: info: applying Makefile.patch dpkg-source: info: applying hardening.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-23996433 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23996433 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23996433 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 gemma dpkg-buildpackage: info: source version 0.98.5+dfsg-1build1 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean install -d /<>/gemma-0.98.5\+dfsg/debian/.debhelper/generated/_source/home make -j4 clean make[1]: Entering directory '/<>' rm -vf ./src/*.o rm -vf ./src/*~ rm -vf ./test/src/*.o rm -vf ./bin/gemma rm -vf ./bin/unittests-gemma make[1]: Leaving directory '/<>' debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/gemma.substvars debian/gemma-doc.substvars debian/files rm -fr -- debian/gemma/ debian/tmp/ debian/gemma-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) rm -f *.log rm -rf test/output/ rm -f bin/gemma make[1]: Leaving directory '/<>' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure install -d /<>/gemma-0.98.5\+dfsg/debian/.debhelper/generated/_source/home dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmm.o src/bslmm.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/bslmmdap.o src/bslmmdap.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/debug.o src/debug.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/fastblas.o src/fastblas.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma.o src/gemma.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gemma_io.o src/gemma_io.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/gzstream.o src/gzstream.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lapack.o src/lapack.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/ldr.o src/ldr.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lm.o src/lm.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/lmm.o src/lmm.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/logistic.o src/logistic.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/main.o src/main.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/mathfunc.o src/mathfunc.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/mvlmm.o src/mvlmm.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/param.o src/param.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/prdt.o src/prdt.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/varcov.o src/varcov.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o src/vc.o src/vc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -DNDEBUG -O3 -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc src/bslmm.o src/bslmmdap.o src/debug.o src/fastblas.o src/gemma.o src/gemma_io.o src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o src/main.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lgsl -lz -lopenblas -o ./bin/gemma -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test --no-parallel make -j1 check make[2]: Entering directory '/<>' g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o test/src/unittests-main.o test/src/unittests-main.cpp g++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/catch -I/usr/include/eigen -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -c -o test/src/unittests-math.o test/src/unittests-math.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DOPENBLAS -isystem/usr/local/opt/openblas/include -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc -Og -Wfatal-errors -g -DHAVE_INLINE -pthread -Wall -std=gnu++11 -Icontrib/catch-1.9.7 -Isrc ./test/src/unittests-main.o ./test/src/unittests-math.o src/bslmm.o src/bslmmdap.o src/debug.o src/fastblas.o src/gemma.o src/gemma_io.o src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lgsl -lz -lopenblas -o ./bin/unittests-gemma -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now ./bin/unittests-gemma Mismatch coordinates (1,0)0:3! This example computes real matrix C=alpha*A*B+beta*C using Intel(R) MKL function dgemm, where A, B, and C are matrices and alpha and beta are double precision scalars Initializing data for matrix multiplication C=A*B for matrix A(2000x200) and matrix B(200x1000) Allocating memory for matrices aligned on 64-byte boundary for better performance Intializing matrix data Computing matrix product using Intel(R) MKL dgemm function via CBLAS interface This example computes real matrix C=alpha*A*B+beta*C using Intel(R) MKL function dgemm, where A, B, and C are matrices and alpha and beta are double precision scalars Initializing data for matrix multiplication C=A*B for matrix A(2000x200) and matrix B(200x1000) Allocating memory for matrices aligned on 64-byte boundary for better performance Intializing matrix data Computing matrix product using Intel(R) MKL dgemm function via CBLAS interface Computations completed. =============================================================================== All tests passed (23 assertions in 4 test cases) rm -vf output/* ruby -Eutf-8 -Itest ./test/dev_tests.rb | tee ./dev_test.log Run options: --seed 29203 # Running: GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 ## number of phenotypes = 1 ## number of total SNPs/var = 7320 ## number of analyzed SNPs = 7317 Calculating Relatedness Matrix ... 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% **** WARNING: Mismatch coordinates (24,0)-0:-0! K is not symmetric! in src/gemma.cpp at line 1913 in BatchRun **** INFO: Done. GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 ## number of phenotypes = 1 ## number of total SNPs/var = 7320 ## number of analyzed SNPs = 7317 Start Eigen-Decomposition... pve estimate =0.00100086 se(pve) =0.204165 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% **** INFO: Done. GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 198 ## number of analyzed individuals = 67 ## number of covariates = 3 ## number of phenotypes = 1 ## number of total SNPs/var = 7320 ## number of analyzed SNPs = 7317 Start Eigen-Decomposition... pve estimate =0.00100086 se(pve) =0.204165 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% ================================================== 100% **** INFO: Done. .GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... ## number of total individuals = 427 ## number of analyzed individuals = 427 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 358499 ## number of analyzed SNPs = 273349 Calculating Relatedness Matrix ... 0% 0% 1% 1% 1% 1% 2% 2% = 2% = 3% = 3% = 3% = 3% = 4% = 4% == 4% == 4% == 5% == 5% == 5% == 6% == 6% === 6% === 6% === 7% === 7% === 7% === 8% === 8% ==== 8% ==== 8% ==== 9% ==== 9% ==== 9% ==== 9% ==== 10% ===== 10% ===== 10% ===== 11% ===== 11% ===== 11% ===== 11% ===== 12% ===== 12% ====== 12% ====== 13% ====== 13% ====== 13% ====== 13% ====== 14% ====== 14% ======= 14% ======= 15% ======= 15% ======= 15% ======= 15% ======= 16% ======= 16% ======== 16% ======== 16% ======== 17% ======== 17% ======== 17% ======== 18% ======== 18% ========= 18% ========= 18% ========= 19% ========= 19% ========= 19% ========= 20% ========= 20% ========== 20% 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GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** INFO: no intercept term is found in the cvt file: a column of 1s is added. ## number of total individuals = 427 ## number of analyzed individuals = 427 ## number of covariates = 2 ## number of phenotypes = 1 ## number of total SNPs/var = 358499 ## number of analyzed SNPs = 223242 Start Eigen-Decomposition... pve estimate =0.365545 se(pve) =0.47481 0% 0% 1% 1% 1% 1% 2% 2% = 2% = 3% = 3% = 3% = 3% = 4% = 4% == 4% == 4% == 5% == 5% == 5% == 6% == 6% === 6% === 6% === 7% === 7% === 7% === 8% === 8% ==== 8% ==== 8% ==== 9% ==== 9% ==== 9% ==== 9% ==== 10% ===== 10% ===== 10% ===== 11% ===== 11% ===== 11% ===== 11% ===== 12% ===== 12% ====== 12% ====== 13% ====== 13% ====== 13% ====== 13% ====== 14% ====== 14% ======= 14% ======= 15% ======= 15% ======= 15% ======= 15% ======= 16% ======= 16% 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================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 GSL_RNG_SEED=100 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... **** TEST MODE: trim individuals from 1940 to 400 **** TEST MODE: trim individuals from 1940 to 400 ## number of total individuals = 400 ## number of analyzed individuals = 247 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of considered SNPS = 1000 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 889 Start Eigen-Decomposition... pve estimate =0.678775 se(pve) =0.0717914 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. . Finished in 109.527591s, 0.0365 runs/s, 0.1917 assertions/s. 4 runs, 21 assertions, 0 failures, 0 errors, 0 skips make[2]: Leaving directory '/<>' rm -fr -- /tmp/dh-xdg-rundir-_f0JIJaN make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/gemma.substvars debian/gemma-doc.substvars rm -fr -- debian/.debhelper/generated/gemma/ debian/gemma/ debian/tmp/ debian/.debhelper/generated/gemma-doc/ debian/gemma-doc/ dh_auto_install install -d /<>/gemma-0.98.5\+dfsg/debian/tmp dh_install install -d debian/gemma/usr/bin cp --reflink=auto -a ./bin/gemma debian/gemma/usr/bin/ install -d debian/.debhelper/generated/gemma install -d debian/.debhelper/generated/gemma-doc dh_installdocs install -d debian/gemma/usr/share/doc/gemma cp --reflink=auto -a ./RELEASE-NOTES.md debian/gemma/usr/share/doc/gemma cp --reflink=auto -a ./README.md debian/gemma/usr/share/doc/gemma chmod -R u\+rw,go=rX debian/gemma/usr/share/doc install -p -m0644 debian/copyright debian/gemma/usr/share/doc/gemma/copyright install -d debian/gemma-doc/usr/share/doc/gemma-doc install -d debian/gemma-doc/usr/share/doc/gemma cd './example/..' && find 'example' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /<>/debian/gemma-doc/usr/share/doc/gemma chmod -R u\+rw,go=rX debian/gemma-doc/usr/share/doc install -p -m0644 debian/copyright debian/gemma-doc/usr/share/doc/gemma-doc/copyright dh_installchangelogs install -p -m0644 debian/changelog debian/gemma/usr/share/doc/gemma/changelog.Debian install -p -m0644 debian/changelog debian/gemma-doc/usr/share/doc/gemma-doc/changelog.Debian dh_perl dh_link dh_strip_nondeterminism Using 1638898254 as canonical time Normalizing debian/gemma-doc/usr/share/doc/gemma/example/BXD_geno.txt.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/gemma-doc/usr/share/doc/gemma/example/mouse_hs1940.geno.txt.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/gemma cd debian/gemma-doc chmod a-x usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian chmod a-x usr/share/doc/gemma-doc/changelog.Debian usr/share/doc/gemma/example/BXD_snps.txt usr/share/doc/gemma/example/HLC.bed usr/share/doc/gemma/example/HLC.bim usr/share/doc/gemma/example/HLC.fam usr/share/doc/gemma/example/HLC.simu.pheno.txt usr/share/doc/gemma/example/demo.txt usr/share/doc/gemma/example/mouse_hs1940.anno.txt usr/share/doc/gemma/example/mouse_hs1940.bed usr/share/doc/gemma/example/mouse_hs1940.bim usr/share/doc/gemma/example/mouse_hs1940.fam usr/share/doc/gemma/example/mouse_hs1940.pheno.txt usr/share/doc/gemma/example/mouse_hs1940_snps.txt usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt gzip -9nf usr/share/doc/gemma-doc/changelog.Debian usr/share/doc/gemma/example/BXD_snps.txt usr/share/doc/gemma/example/HLC.bed usr/share/doc/gemma/example/HLC.bim usr/share/doc/gemma/example/HLC.fam usr/share/doc/gemma/example/HLC.simu.pheno.txt usr/share/doc/gemma/example/demo.txt usr/share/doc/gemma/example/mouse_hs1940.anno.txt usr/share/doc/gemma/example/mouse_hs1940.bed usr/share/doc/gemma/example/mouse_hs1940.bim usr/share/doc/gemma/example/mouse_hs1940.fam usr/share/doc/gemma/example/mouse_hs1940.pheno.txt usr/share/doc/gemma/example/mouse_hs1940_snps.txt usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt gzip -9nf usr/share/doc/gemma/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian cd '/<>' cd '/<>' dh_fixperms find debian/gemma ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/gemma-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/gemma/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/gemma-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/gemma-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/gemma -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/gemma/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/gemma-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing dh_dwz -a dwz -- debian/gemma/usr/bin/gemma dh_strip -a debugedit --build-id --build-id-seed=gemma/0.98.5\+dfsg-1build1 debian/gemma/usr/bin/gemma ef671b4cc7ed07e917a552e848729c7c8b49a60a install -d debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/ef objcopy --only-keep-debug --compress-debug-sections debian/gemma/usr/bin/gemma debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/ef/671b4cc7ed07e917a552e848729c7c8b49a60a.debug chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/ef/671b4cc7ed07e917a552e848729c7c8b49a60a.debug strip --remove-section=.comment --remove-section=.note -o /tmp/MmrOjfugc5/stripMQXquF debian/gemma/usr/bin/gemma chmod --reference debian/gemma/usr/bin/gemma /tmp/MmrOjfugc5/stripMQXquF cat '/tmp/MmrOjfugc5/stripMQXquF' > 'debian/gemma/usr/bin/gemma' chmod --reference /tmp/MmrOjfugc5/stripMQXquF debian/gemma/usr/bin/gemma objcopy --add-gnu-debuglink debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/ef/671b4cc7ed07e917a552e848729c7c8b49a60a.debug debian/gemma/usr/bin/gemma /tmp/MmrOjfugc5/objcopyKEkBnI chmod --reference debian/gemma/usr/bin/gemma /tmp/MmrOjfugc5/objcopyKEkBnI cat '/tmp/MmrOjfugc5/objcopyKEkBnI' > 'debian/gemma/usr/bin/gemma' chmod --reference /tmp/MmrOjfugc5/objcopyKEkBnI debian/gemma/usr/bin/gemma rm -fr debian/.debhelper/gemma/dbgsym-root dh_makeshlibs -a rm -f debian/gemma/DEBIAN/shlibs dh_shlibdeps -a install -d debian/gemma/DEBIAN dpkg-shlibdeps -Tdebian/gemma.substvars debian/gemma/usr/bin/gemma dh_installdeb install -d debian/gemma-doc/DEBIAN dh_gencontrol echo misc:Depends= >> debian/gemma.substvars echo misc:Pre-Depends= >> debian/gemma.substvars dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -Pdebian/gemma echo misc:Depends= >> debian/gemma-doc.substvars echo misc:Pre-Depends= >> debian/gemma-doc.substvars dpkg-gencontrol -pgemma-doc -ldebian/changelog -Tdebian/gemma-doc.substvars -Pdebian/gemma-doc chmod 0644 -- debian/gemma/DEBIAN/control chmod 0644 -- debian/gemma-doc/DEBIAN/control dh_md5sums cd debian/gemma >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/gemma-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/gemma/DEBIAN/md5sums chmod 0644 -- debian/gemma-doc/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/gemma .. dpkg-deb --root-owner-group --build debian/gemma-doc .. INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing gemma-doc (in debian/gemma-doc); do_strip: , oemstrip: pkgstriptranslations: processing gemma (in debian/gemma); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/gemma-doc/DEBIAN/control, package gemma-doc, directory debian/gemma-doc INFO: pkgstripfiles: waiting for lock (gemma-doc) ... pkgstripfiles: processing control file: debian/gemma/DEBIAN/control, package gemma, directory debian/gemma pkgstripfiles: Truncating usr/share/doc/gemma/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package gemma ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gemma' in '../gemma_0.98.5+dfsg-1build1_amd64.deb'. pkgstripfiles: Truncating usr/share/doc/gemma-doc/changelog.Debian.gz to topmost ten records pkgstripfiles: Disabled PNG optimization for -doc package gemma-doc (to save build time) dpkg-deb: building package 'gemma-doc' in '../gemma-doc_0.98.5+dfsg-1build1_all.deb'. dpkg-genbuildinfo --build=binary -O../gemma_0.98.5+dfsg-1build1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../gemma_0.98.5+dfsg-1build1_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 2022-06-22T12:54:21Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gemma_0.98.5+dfsg-1build1_amd64.changes: ---------------------------------------- Format: 1.8 Date: Tue, 07 Dec 2021 17:30:54 +0000 Source: gemma Binary: gemma gemma-doc Built-For-Profiles: noudeb Architecture: all amd64 Version: 0.98.5+dfsg-1build1 Distribution: kinetic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: gemma - Genome-wide Efficient Mixed Model Association gemma-doc - Example folder for GEMMA Changes: gemma (0.98.5+dfsg-1build1) jammy; urgency=medium . * No-change rebuild against libgsl27 Checksums-Sha1: b899341186108f9c2d9e6b48092439832f3b261f 33395830 gemma-doc_0.98.5+dfsg-1build1_all.deb bdd1427ebc853e5ed50285ea1a96c65d31bd6d71 6899 gemma_0.98.5+dfsg-1build1_amd64.buildinfo 3a20548ef4afe023256d61b3cce4105bbebd8fea 364656 gemma_0.98.5+dfsg-1build1_amd64.deb Checksums-Sha256: 31a7c0f4519e97924e42e6b4cc2719e8c6da04a8fbeb5f3855ba1136bea7fdda 33395830 gemma-doc_0.98.5+dfsg-1build1_all.deb 45ef9b14b022409ad928dd58934f6f65c204f5ff21381fb3fa7e7cfc42d057f6 6899 gemma_0.98.5+dfsg-1build1_amd64.buildinfo 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bd90e08d219fc56595c8a00131825a6a 364656 gemma_0.98.5+dfsg-1build1_amd64.deb Checksums-Sha1: b899341186108f9c2d9e6b48092439832f3b261f 33395830 gemma-doc_0.98.5+dfsg-1build1_all.deb 3a20548ef4afe023256d61b3cce4105bbebd8fea 364656 gemma_0.98.5+dfsg-1build1_amd64.deb Checksums-Sha256: 31a7c0f4519e97924e42e6b4cc2719e8c6da04a8fbeb5f3855ba1136bea7fdda 33395830 gemma-doc_0.98.5+dfsg-1build1_all.deb a6e4c4c34a5288a5c143d0a2cb6440fe8bfea67ccaa82d196b178f465e8d501f 364656 gemma_0.98.5+dfsg-1build1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Wed, 22 Jun 2022 12:54:20 +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), ca-certificates (= 20211016), catch (= 1.12.1-1.1ubuntu1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-3ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-3build1), debconf (= 1.5.79ubuntu1), debhelper (= 13.7.1ubuntu1), debianutils (= 5.7-0.2), debugedit (= 1:5.0-4build1), dh-autoreconf (= 20), 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), 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), gfortran (= 4:11.2.0-1ubuntu1), gfortran-11 (= 11.3.0-3ubuntu1), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.10-4ubuntu4), hostname (= 3.23ubuntu2), init-system-helpers (= 1.63), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), 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), libbsd0 (= 0.11.6-1), 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 (= 0.7.9-4), 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), 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), libedit2 (= 3.1-20210910-1build1), libeigen3-dev (= 3.4.0-2ubuntu2), libelf1 (= 0.187-1), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), 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), libgfortran-11-dev (= 11.3.0-3ubuntu1), libgfortran5 (= 12.1.0-2ubuntu1), libglib2.0-0 (= 2.72.2-2), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgomp1 (= 12.1.0-2ubuntu1), libgpg-error0 (= 1.45-2), libgprofng0 (= 2.38.50.20220615-4ubuntu1), libgsl-dev (= 2.7.1+dfsg-3), libgsl27 (= 2.7.1+dfsg-3), libgslcblas0 (= 2.7.1+dfsg-3), libgssapi-krb5-2 (= 1.19.2-2), libicu71 (= 71.1-3), libisl23 (= 0.24-2build1), libitm1 (= 12.1.0-2ubuntu1), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-3ubuntu1), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), 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), libmd0 (= 1.0.4-1build1), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libopenblas-dev (= 0.3.20+ds-2), libopenblas-pthread-dev (= 0.3.20+ds-2), libopenblas0 (= 0.3.20+ds-2), libopenblas0-pthread (= 0.3.20+ds-2), libpam-modules (= 1.4.0-13ubuntu1), libpam-modules-bin (= 1.4.0-13ubuntu1), libpam-runtime (= 1.4.0-13ubuntu1), libpam0g (= 1.4.0-13ubuntu1), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-3ubuntu1), libpipeline1 (= 1.5.6-1), libquadmath0 (= 12.1.0-2ubuntu1), libruby3.0 (= 3.0.2-7ubuntu2), libseccomp2 (= 2.5.4-1ubuntu1), libselinux1 (= 3.4-1), libsigsegv2 (= 2.13-1ubuntu3), libsmartcols1 (= 2.38-4ubuntu1), libssl3 (= 3.0.3-5ubuntu3), libstdc++-11-dev (= 11.3.0-3ubuntu1), libstdc++6 (= 12.1.0-2ubuntu1), libsub-override-perl (= 0.09-3), libsystemd0 (= 249.11-0ubuntu4), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtool (= 2.4.7-4), libtsan0 (= 11.3.0-3ubuntu1), libubsan1 (= 12.1.0-2ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 249.11-0ubuntu4), libunistring2 (= 1.0-1), libuuid1 (= 2.38-4ubuntu1), libxml2 (= 2.9.14+dfsg-1), libyaml-0-2 (= 0.2.2-1build2), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.15.0-27.28), login (= 1:4.11.1+dfsg1-2ubuntu1), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 27), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), openssl (= 3.0.3-5ubuntu3), patch (= 2.7.6-7build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), pkg-config (= 0.29.2-1ubuntu3), po-debconf (= 1.0.21+nmu1), rake (= 13.0.6-3), rpcsvc-proto (= 1.4.2-0ubuntu6), ruby (= 1:3.0~exp1), ruby-net-telnet (= 0.1.1-2.1), ruby-rubygems (= 3.3.15-1), ruby-webrick (= 1.7.0-3), ruby-xmlrpc (= 0.3.2-2), ruby3.0 (= 3.0.2-7ubuntu2), rubygems-integration (= 1.18), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), shunit2 (= 2.1.6-1.2), 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="1638898254" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gemma-doc_0.98.5+dfsg-1build1_all.deb ------------------------------------- new Debian package, version 2.0. size 33395830 bytes: control archive=1088 bytes. 509 bytes, 15 lines control 1686 bytes, 21 lines md5sums Package: gemma-doc Source: gemma Version: 0.98.5+dfsg-1build1 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 33079 Recommends: gemma Section: doc Priority: optional Multi-Arch: foreign Homepage: https://www.xzlab.org/software.html Description: Example folder for GEMMA This package ships example data for the Genome-wide Efficient Mixed Model Association. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2021-12-07 17:30 ./ drwxr-xr-x root/root 0 2021-12-07 17:30 ./usr/ drwxr-xr-x root/root 0 2021-12-07 17:30 ./usr/share/ drwxr-xr-x root/root 0 2021-12-07 17:30 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-12-07 17:30 ./usr/share/doc/gemma-doc/ -rw-r--r-- root/root 1087 2021-12-07 17:30 ./usr/share/doc/gemma-doc/changelog.Debian.gz -rw-r--r-- root/root 2231 2021-10-06 05:45 ./usr/share/doc/gemma-doc/copyright drwxr-xr-x root/root 0 2021-12-07 17:30 ./usr/share/doc/gemma/ drwxr-xr-x root/root 0 2021-12-07 17:30 ./usr/share/doc/gemma/example/ -rw-r--r-- root/root 2010 2021-08-25 12:14 ./usr/share/doc/gemma/example/BXD_covariates.txt -rw-r--r-- root/root 2010 2021-08-25 12:14 ./usr/share/doc/gemma/example/BXD_covariates2.txt -rw-r--r-- root/root 122816 2021-12-07 17:30 ./usr/share/doc/gemma/example/BXD_geno.txt.gz -rw-r--r-- root/root 800 2021-08-25 12:14 ./usr/share/doc/gemma/example/BXD_pheno.txt -rw-r--r-- root/root 68896 2021-08-25 12:14 ./usr/share/doc/gemma/example/BXD_snps.txt.gz -rw-r--r-- root/root 23388913 2021-08-25 12:14 ./usr/share/doc/gemma/example/HLC.bed.gz -rw-r--r-- root/root 3214181 2021-08-25 12:14 ./usr/share/doc/gemma/example/HLC.bim.gz -rw-r--r-- root/root 1976 2021-08-25 12:14 ./usr/share/doc/gemma/example/HLC.fam.gz -rw-r--r-- root/root 37341 2021-08-25 12:14 ./usr/share/doc/gemma/example/HLC.simu.pheno.txt.gz -rw-r--r-- root/root 3857 2021-08-25 12:14 ./usr/share/doc/gemma/example/HLC_covariates.txt -rw-r--r-- root/root 2260 2021-08-25 12:14 ./usr/share/doc/gemma/example/demo.txt.gz -rw-r--r-- root/root 144965 2021-08-25 12:14 ./usr/share/doc/gemma/example/mouse_hs1940.anno.txt.gz -rw-r--r-- root/root 1309648 2021-08-25 12:14 ./usr/share/doc/gemma/example/mouse_hs1940.bed.gz -rw-r--r-- root/root 155001 2021-08-25 12:14 ./usr/share/doc/gemma/example/mouse_hs1940.bim.gz -rw-r--r-- root/root 47758 2021-08-25 12:14 ./usr/share/doc/gemma/example/mouse_hs1940.fam.gz -rw-r--r-- root/root 5302346 2021-12-07 17:30 ./usr/share/doc/gemma/example/mouse_hs1940.geno.txt.gz -rw-r--r-- root/root 29612 2021-08-25 12:14 ./usr/share/doc/gemma/example/mouse_hs1940.pheno.txt.gz -rw-r--r-- root/root 4231 2021-08-25 12:14 ./usr/share/doc/gemma/example/mouse_hs1940_snps.txt.gz -rw-r--r-- root/root 14066 2021-08-25 12:14 ./usr/share/doc/gemma/example/mouse_hs1940_snps_anno.txt.gz gemma_0.98.5+dfsg-1build1_amd64.deb ----------------------------------- new Debian package, version 2.0. size 364656 bytes: control archive=1300 bytes. 2025 bytes, 35 lines control 327 bytes, 5 lines md5sums Package: gemma Version: 0.98.5+dfsg-1build1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 942 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libgsl27 (>= 2.7.1), libopenblas0, libstdc++6 (>= 11), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://www.xzlab.org/software.html Description: Genome-wide Efficient Mixed Model Association GEMMA is the software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS): . * It fits a univariate linear mixed model (LMM) for marker association tests with a single phenotype to account for population stratification and sample structure, and for estimating the proportion of variance in phenotypes explained (PVE) by typed genotypes (i.e. "chip heritability"). * It fits a multivariate linear mixed model (mvLMM) for testing marker associations with multiple phenotypes simultaneously while controlling for population stratification, and for estimating genetic correlations among complex phenotypes. * It fits a Bayesian sparse linear mixed model (BSLMM) using Markov chain Monte Carlo (MCMC) for estimating PVE by typed genotypes, predicting phenotypes, and identifying associated markers by jointly modeling all markers while controlling for population structure. * It estimates variance component/chip heritability, and partitions it by different SNP functional categories. In particular, it uses HE regression or REML AI algorithm to estimate variance components when individual-level data are available. It uses MQS to estimate variance components when only summary statisics are available. . GEMMA is computationally efficient for large scale GWAS and uses freely available open-source numerical libraries. 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