Mon Aug 9 14:00:28 UTC 2021 I: starting to build gemma/bullseye/arm64 on jenkins on '2021-08-09 14:00' Mon Aug 9 14:00:28 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_25/40573/console.log Mon Aug 9 14:00:28 UTC 2021 I: Downloading source for bullseye/gemma=0.98.4+dfsg-4 --2021-08-09 14:00:28-- http://cdn-fastly.deb.debian.org/debian/pool/main/g/gemma/gemma_0.98.4+dfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2113 (2.1K) Saving to: ‘gemma_0.98.4+dfsg-4.dsc’ 0K .. 100% 319M=0s 2021-08-09 14:00:28 (319 MB/s) - ‘gemma_0.98.4+dfsg-4.dsc’ saved [2113/2113] Mon Aug 9 14:00:28 UTC 2021 I: gemma_0.98.4+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: gemma Binary: gemma, gemma-doc Architecture: any all Version: 0.98.4+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://www.xzlab.org/software.html Standards-Version: 4.5.1 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 Package-List: gemma deb science optional arch=any gemma-doc deb doc optional arch=all Checksums-Sha1: 85c82ad902b91a62f37dc6db462f178ed64c156c 42535920 gemma_0.98.4+dfsg.orig.tar.xz 35d27754373e23bdb5dbc1bf52f8f4aae6dc4e55 6412 gemma_0.98.4+dfsg-4.debian.tar.xz Checksums-Sha256: ea2833c102e94894b5b6c65f6d9deaa717cc4502e842057f594273bf36fbd702 42535920 gemma_0.98.4+dfsg.orig.tar.xz 2df2ed606edbb7ba24ea56b277b7ec8954d3c5587d3faa92102e35d52805873d 6412 gemma_0.98.4+dfsg-4.debian.tar.xz Files: 81a168398df11339385afb0643057463 42535920 gemma_0.98.4+dfsg.orig.tar.xz ae27d59ef00df2077b46517b54ba989b 6412 gemma_0.98.4+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmEE3XQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGv9hAAhhxHSFPnj7NaC3XEuSePuaSfOUf43Fwu HbKUtytAmxKH0s65ruiMyfxJJRXmWxNH1RERPAErQTfQ+SsotQeVyrRa2/mwy2G7 3xYMznne9bjDYM4PSgds7Q6JayEaSLrbjsSMGH/9TLVopFSvI2hJj6cvwsdgtgBy NaUWNwy7PTX1S8Mcmru0hbVkNtH9HiVbOloMFmKkXs3FWMEowZaoqJ7ZXfpK1/Ks vl5Iix75LOGhBPnJfriWC3pNDscDczdIezSy2KbVGpHbydfbxu2mmjGh8Au5Dm7X ykqctlhzl2+P/L+e2Ys2kzigZm64V7+V6+glyGB+DWBF/gBl7kfh7Uip/1b/yo3q LPT/Rkz+6Iqu0OQIZVsTNmuGaD+QGcGRidaj6qqSroaHYRZiyIKfLi+Z2MlNhI+D FskhKe7bKxmcK49UAzp7w7eTHp1h2sPUtPFsEPM8fhWHFBESVlj7L22SzHi8ud0z gjEatmQc34UeFE4sqP94BNcpxqJfRKkV1lKddIhP8oAD5CRXS1TMtT5Stvazcscm Ub1N4HSPGVjS1R1EWsuKZX2ZM2jAaNV85giDEsFj55679wd97k9/NsbQnOf5vco+ xdAu10gu4R5wbpx/SRr70AvXlfaEGVl3izrx4EYdV0qU0rDYOcbh+bn4prKstcff gPWxnoh+Ivc= =u3S7 -----END PGP SIGNATURE----- Mon Aug 9 14:00:28 UTC 2021 I: Checking whether the package is not for us Mon Aug 9 14:00:29 UTC 2021 I: Starting 1st build on remote node codethink15-arm64.debian.net. Mon Aug 9 14:00:29 UTC 2021 I: Preparing to do remote build '1' on codethink15-arm64.debian.net. Mon Aug 9 14:18:27 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Sep 11 08:23:37 -12 2022 I: pbuilder-time-stamp: 1662927817 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gemma_0.98.4+dfsg-4.dsc] I: copying [./gemma_0.98.4+dfsg.orig.tar.xz] I: copying [./gemma_0.98.4+dfsg-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.Q3shv1Ui/trustedkeys.kbx': General error gpgv: Signature made Fri Jul 30 17:19:48 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gemma_0.98.4+dfsg-4.dsc dpkg-source: info: extracting gemma in gemma-0.98.4+dfsg dpkg-source: info: unpacking gemma_0.98.4+dfsg.orig.tar.xz dpkg-source: info: unpacking gemma_0.98.4+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying exclude_assertions_failing_under_some_circumstances.patch dpkg-source: info: applying Reproducible_builds.patch dpkg-source: info: applying no-lquadmath.patch dpkg-source: info: applying Makefile.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/8191/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='8191' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.6ZQsnZwvoE/pbuilderrc_Fhvz --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.6ZQsnZwvoE/b1 --logfile b1/build.log gemma_0.98.4+dfsg-4.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink15-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 28 2021 more -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 10 03:46 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jul 28 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/8191/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libopenblas-dev; however: Package libopenblas-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on catch; however: Package catch is not installed. pbuilder-satisfydepends-dummy depends on shunit2; however: Package shunit2 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} catch{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-10{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libeigen3-dev{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran-10-dev{a} libgfortran5{a} libglib2.0-0{a} libgsl-dev{a} libgsl25{a} libgslcblas0{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} po-debconf{a} sensible-utils{a} shunit2{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 38.9 MB of archives. After unpacking 177 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 catch arm64 1.12.1-1.1 [114 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libgfortran-10-dev arm64 10.2.1-6 [388 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 gfortran-10 arm64 10.2.1-6 [8654 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 gfortran arm64 4:10.2.1-1 [1424 B] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libeigen3-dev all 3.3.9-2 [858 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libgslcblas0 arm64 2.6+dfsg-2 [73.4 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libgsl25 arm64 2.6+dfsg-2 [812 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libgsl-dev arm64 2.6+dfsg-2 [1006 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libopenblas0-pthread arm64 0.3.13+ds-3 [3961 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libopenblas0 arm64 0.3.13+ds-3 [32.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libopenblas-pthread-dev arm64 0.3.13+ds-3 [3123 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libopenblas-dev arm64 0.3.13+ds-3 [44.1 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 shunit2 all 2.1.6-1.2 [39.7 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Fetched 38.9 MB in 1s (53.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. 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Setting up libmagic1:arm64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libgfortran5:arm64 (10.2.1-6) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up catch (1.12.1-1.1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libgfortran-10-dev:arm64 (10.2.1-6) ... Setting up libelf1:arm64 (0.183-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libopenblas0-pthread:arm64 (0.3.13+ds-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/aarch64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-aarch64-linux-gnu) in auto mode Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libeigen3-dev (3.3.9-2) ... Setting up gfortran-10 (10.2.1-6) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libopenblas0:arm64 (0.3.13+ds-3) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libopenblas-pthread-dev:arm64 (0.3.13+ds-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/aarch64-linux-gnu/libopenblas.so (libopenblas.so-aarch64-linux-gnu) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:10.2.1-1) ... 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:arm64 (0.3.13+ds-3) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/gemma-0.98.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gemma_0.98.4+dfsg-4_source.changes dpkg-buildpackage: info: source package gemma dpkg-buildpackage: info: source version 0.98.4+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean install -d /build/gemma-0.98.4\+dfsg/debian/.debhelper/generated/_source/home make -j8 clean make[1]: Entering directory '/build/gemma-0.98.4+dfsg' 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 '/build/gemma-0.98.4+dfsg' debian/rules override_dh_clean make[1]: Entering directory '/build/gemma-0.98.4+dfsg' 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 '/build/gemma-0.98.4+dfsg' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure install -d /build/gemma-0.98.4\+dfsg/debian/.debhelper/generated/_source/home dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/gemma-0.98.4+dfsg' g++ -g -O2 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 src/debug.cpp:61:44: warning: extra ';' [-Wpedantic] 61 | bool is_debug_mode() { return debug_mode; }; | ^ src/debug.cpp:62:54: warning: extra ';' [-Wpedantic] 62 | bool is_debug_data_mode() { return debug_data_mode; }; | ^ src/debug.cpp:63:49: warning: extra ';' [-Wpedantic] 63 | bool is_no_check_mode() { return !debug_check; }; | ^ src/debug.cpp:64:45: warning: extra ';' [-Wpedantic] 64 | bool is_check_mode() { return debug_check; }; | ^ src/debug.cpp:65:53: warning: extra ';' [-Wpedantic] 65 | bool is_fpe_check_mode() { return debug_fpe_check; }; | ^ src/debug.cpp:66:47: warning: extra ';' [-Wpedantic] 66 | bool is_strict_mode() { return debug_strict; }; | ^ src/debug.cpp:67:45: warning: extra ';' [-Wpedantic] 67 | bool is_quiet_mode() { return debug_quiet; }; | ^ src/debug.cpp:68:59: warning: extra ';' [-Wpedantic] 68 | bool is_issue(uint issue) { return issue == debug_issue; }; | ^ src/debug.cpp:69:47: warning: extra ';' [-Wpedantic] 69 | bool is_legacy_mode() { return debug_legacy; }; | ^ g++ -g -O2 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 make[1]: Leaving directory '/build/gemma-0.98.4+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/gemma-0.98.4+dfsg' dh_auto_test --no-parallel make -j1 check make[2]: Entering directory '/build/gemma-0.98.4+dfsg' g++ -g -O2 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 -fdebug-prefix-map=/build/gemma-0.98.4+dfsg=. -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 ./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 test/output/* cd test && ./dev_test_suite.sh | tee ../dev_test.log run system shunit2 testLinearModel GEMMA 0.98.4 (2021-01-29) by Xiang Zhou 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 = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10768 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. ## total computation time = 0.138176 min testBXDStandardRelatednessMatrixKSingularError GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 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. GSL ERROR: matrix is singular in lu.c at line 449 errno 1 testBXDStandardRelatednessMatrixK GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 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% **** INFO: Done. testBXDLMLikelihoodRatio GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 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 0% ====== 14% ============= 27% ==================== 41% =========================== 55% ================================== 68% ======================================== 82% =============================================== 96% ================================================== 100% **** INFO: Done. testBXDLMMLikelihoodRatio GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 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. testBXDLMM9LikelihoodRatio GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 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. testCenteredRelatednessMatrixissue188 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou 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 = 1008 ## number of analyzed individuals = 876 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 2000 ## number of analyzed SNPs = 1850 Calculating Relatedness Matrix ... 0% ========================= 50% ================================================== 100% **** WARNING: K has 75 eigenvalues close to zero in src/gemma.cpp at line 1912 **** WARNING: K is ill conditioned! in src/gemma.cpp at line 1912 **** INFO: Done. testLMMissue188 GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... ## number of total individuals = 1008 ## number of analyzed individuals = 876 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 2000 ## number of analyzed SNPs = 1850 **** WARNING: K has 3 eigenvalues close to zero in src/gemma.cpp at line 2590 **** WARNING: K is ill conditioned! in src/gemma.cpp at line 2590 Start Eigen-Decomposition... **** WARNING: Matrix G has 3 eigenvalues close to zero pve estimate =0.631857 se(pve) =0.0548406 0% ========================= 50% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixKLOCO1 GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 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 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. ## total computation time = 0.108544 min testUnivariateLinearMixedModelLOCO1 GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 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. ## total computation time = 0.0471874 min testPlinkCenteredRelatednessMatrixKLOCO1 testPlinkUnivariateLinearMixedModelLOCO1 testCorrelatedPhenotypesMvLLM GSL_RNG_SEED=100 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440 Reading Files ... ## number of total individuals = 1000 ## number of analyzed individuals = 1000 ## number of covariates = 1 ## number of phenotypes = 5 ## number of total SNPs/var = 100 ## number of analyzed SNPs = 100 REMLE estimate for Vg in the null model: 0.8091 0.1435 0.0660 -0.1456 -0.0664 0.1165 0.0907 0.0362 -0.0830 0.0639 -0.5533 -0.0985 0.1171 -0.0765 0.4131 se(Vg): 0.0736 0.0355 0.0299 0.0421 0.0264 0.0422 0.0444 0.0279 0.0430 0.0479 0.0516 0.0254 0.0295 0.0313 0.0389 REMLE estimate for Ve in the null model: 0.0334 0.0267 0.4502 -0.0529 -0.0883 0.6004 0.0683 0.1413 -0.6502 0.8400 -0.0128 -0.0041 -0.0706 0.0880 0.0419 se(Ve): 0.0378 0.0252 0.0329 0.0299 0.0281 0.0456 0.0332 0.0319 0.0494 0.0583 0.0266 0.0186 0.0215 0.0242 0.0208 REMLE likelihood = -3813.3258 MLE estimate for Vg in the null model: 0.8082 0.1434 0.0660 -0.1455 -0.0664 0.1165 0.0906 0.0362 -0.0830 0.0639 -0.5528 -0.0984 0.1170 -0.0764 0.4127 se(Vg): 0.0735 0.0355 0.0298 0.0420 0.0264 0.0421 0.0443 0.0278 0.0430 0.0478 0.0515 0.0254 0.0295 0.0313 0.0388 MLE estimate for Ve in the null model: 0.0334 0.0267 0.4497 -0.0529 -0.0882 0.5997 0.0682 0.1412 -0.6495 0.8392 -0.0128 -0.0040 -0.0705 0.0879 0.0418 se(Ve): 0.0378 0.0252 0.0329 0.0298 0.0281 0.0455 0.0331 0.0318 0.0493 0.0582 0.0265 0.0185 0.0215 0.0242 0.0207 MLE likelihood = -3814.3913 0% ================================================== 100% **** INFO: Done. Ran 13 tests. OK tail -n 1 dev_test.log | grep -q 'OK' rm -vf test/output/* removed 'test/output/BXD.cXX.txt' removed 'test/output/BXD.log.txt' removed 'test/output/BXD_LMM_LR.assoc.txt' removed 'test/output/BXD_LMM_LR.log.txt' removed 'test/output/BXD_LM_LR.assoc.txt' removed 'test/output/BXD_LM_LR.log.txt' removed 'test/output/corrpheno.assoc.txt' removed 'test/output/corrpheno.log.txt' removed 'test/output/issue188.assoc.txt' removed 'test/output/issue188.cXX.txt' removed 'test/output/issue188.log.txt' removed 'test/output/mouse_hs1940_CD8_LOCO1_lmm.assoc.txt' removed 'test/output/mouse_hs1940_CD8_LOCO1_lmm.log.txt' removed 'test/output/mouse_hs1940_CD8_lm.assoc.txt' removed 'test/output/mouse_hs1940_CD8_lm.log.txt' removed 'test/output/mouse_hs1940_LOCO1.cXX.txt' removed 'test/output/mouse_hs1940_LOCO1.log.txt' cd test && ./test_suite.sh | tee ../test.log run system shunit2 testBslmm1 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 1 (option 1); first value = 1791095845 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10775 Start Eigen-Decomposition... pve estimate =0.590431 se(pve) =0.0480392 Calculating UtX... initial value of h = 0.590431 initial value of rho = 0.41375 initial value of pi = 0.00269142 initial value of |gamma| = 29 0% 0.00 ==== 9% 0.18 ========= 18% 0.18 ============= 27% 0.18 ================== 36% 0.18 ====================== 45% 0.17 =========================== 55% 0.17 =============================== 64% 0.17 ==================================== 73% 0.16 ======================================== 82% 0.16 ============================================= 91% 0.16 ================================================== 100% 0.16 **** INFO: Done. testBslmm2 GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10775 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm3 GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 1 (option 1); first value = 1791095845 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10775 Start Eigen-Decomposition... pve estimate =0.372151 se(pve) =0.0522377 Calculating UtX... initial value of h = 0.372151 initial value of rho = 0.393216 initial value of pi = 0.00194896 initial value of |gamma| = 21 0% 0.00 ==== 9% 0.22 ========= 18% 0.22 ============= 27% 0.21 ================== 36% 0.21 ====================== 45% 0.21 =========================== 55% 0.21 =============================== 64% 0.21 ==================================== 73% 0.21 ======================================== 82% 0.21 ============================================= 91% 0.21 ================================================== 100% 0.21 **** INFO: Done. testBslmm4 GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 Adding Breeding Values ... Start Eigen-Decomposition... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testBslmm5 GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 100 (option 100); first value = 2333906440 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 757 ## number of covariates = 1 ## number of phenotypes = 1 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testCenteredRelatednessMatrixKFullLOCO1 GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testUnivariateLinearMixedModelFullLOCO1 GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## leave one chromosome out (LOCO) = 1 ## number of total SNPs/var = 12226 ## number of SNPS for K = 11182 ## number of SNPS for GWAS = 1044 ## number of analyzed SNPs = 10768 Start Eigen-Decomposition... pve estimate =0.593114 se(pve) =0.0332587 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. ## total computation time = 0.496229 min testCenteredRelatednessMatrixK GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10768 Calculating Relatedness Matrix ... 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testUnivariateLinearMixedModel GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1410 ## number of covariates = 1 ## number of phenotypes = 1 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10768 Start Eigen-Decomposition... pve estimate =0.608801 se(pve) =0.032774 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% ================================================== 100% **** INFO: Done. ## total computation time = 1.2353 min testLinearMixedModelPhenotypes GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL_RNG_SEED=10 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 Reading Files ... ## number of total individuals = 1940 ## number of analyzed individuals = 1197 ## number of covariates = 1 ## number of phenotypes = 2 ## number of total SNPs/var = 12226 ## number of analyzed SNPs = 10758 Start Eigen-Decomposition... REMLE estimate for Vg in the null model: 1.3940 -0.2267 2.0817 se(Vg): 0.1567 0.1363 0.2359 REMLE estimate for Ve in the null model: 0.3489 0.0491 0.4144 se(Ve): 0.0206 0.0166 0.0267 REMLE likelihood = -2855.1664 MLE estimate for Vg in the null model: 1.3959 -0.2267 2.0854 se(Vg): 0.1568 0.1365 0.2361 MLE estimate for Ve in the null model: 0.3483 0.0490 0.4136 se(Ve): 0.0206 0.0166 0.0266 MLE likelihood = -2856.0280 0% ==== 8% ======== 16% ============ 25% ================ 33% ==================== 41% ======================== 49% ============================ 57% ================================ 65% ==================================== 74% ======================================== 82% ============================================ 90% ================================================= 98% ================================================== 100% **** INFO: Done. testPlinkStandardRelatednessMatrixK GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 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% ========== 20% 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================================================== 100% **** INFO: Done. testPlinkLinearMixedModelCovariates GSL_RNG_SEED=10 GEMMA 0.98.4 (2021-01-29) by Xiang Zhou and team (C) 2012-2021 GSL random generator type: mt19937; seed = 10 (option -1); first value = 3312796937 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% 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Ran 12 tests. OK tail -n 1 test.log | grep -q 'OK' test.log make[2]: Leaving directory '/build/gemma-0.98.4+dfsg' rm -fr -- /tmp/dh-xdg-rundir-NBhDGhpx make[1]: Leaving directory '/build/gemma-0.98.4+dfsg' 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 /build/gemma-0.98.4\+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 {} /build/gemma-0.98.4+dfsg/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 1627674837 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 '/build/gemma-0.98.4+dfsg' cd '/build/gemma-0.98.4+dfsg' 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 install -d debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/86 objcopy --only-keep-debug --compress-debug-sections debian/gemma/usr/bin/gemma debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/86/89e7d2e583205bb12b8c8d169bf69585e9e079.debug chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/86/89e7d2e583205bb12b8c8d169bf69585e9e079.debug strip --remove-section=.comment --remove-section=.note debian/gemma/usr/bin/gemma objcopy --add-gnu-debuglink debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/86/89e7d2e583205bb12b8c8d169bf69585e9e079.debug debian/gemma/usr/bin/gemma install -d debian/.debhelper/gemma/dbgsym-root/usr/share/doc ln -s gemma debian/.debhelper/gemma/dbgsym-root/usr/share/doc/gemma-dbgsym 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-doc.substvars echo misc:Pre-Depends= >> debian/gemma-doc.substvars dpkg-gencontrol -pgemma-doc -ldebian/changelog -Tdebian/gemma-doc.substvars -Pdebian/gemma-doc echo misc:Depends= >> debian/gemma.substvars echo misc:Pre-Depends= >> debian/gemma.substvars install -d debian/.debhelper/gemma/dbgsym-root/DEBIAN dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -Pdebian/.debhelper/gemma/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=gemma-dbgsym "-DDepends=gemma (= \${binary:Version})" "-DDescription=debug symbols for gemma" -DBuild-Ids=8689e7d2e583205bb12b8c8d169bf69585e9e079 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/gemma-doc/DEBIAN/control chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/DEBIAN/control dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -Pdebian/gemma chmod 0644 -- debian/gemma/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 cd debian/.debhelper/gemma/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/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/.debhelper/gemma/dbgsym-root .. dpkg-deb: building package 'gemma-dbgsym' in '../gemma-dbgsym_0.98.4+dfsg-4_arm64.deb'. dpkg-deb --root-owner-group --build debian/gemma-doc .. dpkg-deb: building package 'gemma' in '../gemma_0.98.4+dfsg-4_arm64.deb'. dpkg-deb: building package 'gemma-doc' in '../gemma-doc_0.98.4+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gemma_0.98.4+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/8191 and its subdirectories I: Current time: Sun Sep 11 08:41:22 -12 2022 I: pbuilder-time-stamp: 1662928882 Mon Aug 9 14:18:28 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink10-arm64.debian.net. Mon Aug 9 14:18:28 UTC 2021 I: Preparing to do remote build '2' on codethink10-arm64.debian.net. Mon Aug 9 14:39:14 UTC 2021 I: Deleting $TMPDIR on codethink10-arm64.debian.net. Mon Aug 9 14:39:14 UTC 2021 I: gemma_0.98.4+dfsg-4_arm64.changes: Format: 1.8 Date: Fri, 30 Jul 2021 21:53:57 +0200 Source: gemma Binary: gemma gemma-dbgsym gemma-doc Architecture: arm64 all Version: 0.98.4+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gemma - Genome-wide Efficient Mixed Model Association gemma-doc - Example folder for GEMMA Closes: 991652 Changes: gemma (0.98.4+dfsg-4) unstable; urgency=medium . * Team upload. * Apply patch from upstream who explained: changed/disabled some other tests (attached). The problem is that different AMD64 CPUs together with OpenBlas simply give different results (mostly SIMD differences). Closes: #991652 Checksums-Sha1: 37e8bad35550268914d3e9287290de74ef7cc83b 5530928 gemma-dbgsym_0.98.4+dfsg-4_arm64.deb b7a557b628b5a4e23cb3cd88df72383263f5fc44 33411396 gemma-doc_0.98.4+dfsg-4_all.deb 34cc3b023414a53b8c9373abde775d991d74ff96 5661 gemma_0.98.4+dfsg-4_arm64.buildinfo 49bf4e1fc757a108c47a2eb00701737b83828f6a 340156 gemma_0.98.4+dfsg-4_arm64.deb Checksums-Sha256: 9f3163afb5141be7b7304b7f2184b5ed4139a895e53c8932581c164a4db67b17 5530928 gemma-dbgsym_0.98.4+dfsg-4_arm64.deb 48eecacbdd67efe06b85d672533f09fea830ade6f338358069cdae2d09f670df 33411396 gemma-doc_0.98.4+dfsg-4_all.deb ac5583796e2a775a7319172ad43ff665056a07e545b305a277768204f828e258 5661 gemma_0.98.4+dfsg-4_arm64.buildinfo f6489f03331bbb1878a39241ba493cfa6f9e1b4c80dc3776a0b7fb97de238ef2 340156 gemma_0.98.4+dfsg-4_arm64.deb Files: 9523cdc5ee486a718b1ec9a6c2b21801 5530928 debug optional gemma-dbgsym_0.98.4+dfsg-4_arm64.deb e9ec5f6e0beec558c0c9ff3b6a355fe5 33411396 doc optional gemma-doc_0.98.4+dfsg-4_all.deb fea30beedbdef49272d03b86574bcad1 5661 science optional gemma_0.98.4+dfsg-4_arm64.buildinfo bd1508ea85587f303bc6c56d64d95780 340156 science optional gemma_0.98.4+dfsg-4_arm64.deb Mon Aug 9 14:39:15 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.6ZQsnZwvoE/gemma_0.98.4+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.6ZQsnZwvoE/gemma_0.98.4+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.6ZQsnZwvoE/gemma_0.98.4+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.6ZQsnZwvoE/b1/gemma_0.98.4+dfsg-4_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.6ZQsnZwvoE/b2/gemma_0.98.4+dfsg-4_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.711s) 0.711s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.452s) 0.451s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Mon Aug 9 14:39:18 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Mon Aug 9 14:39:18 UTC 2021 I: gemma from bullseye built successfully and reproducibly on arm64. Mon Aug 9 14:39:19 UTC 2021 I: Submitting .buildinfo files to external archives: Mon Aug 9 14:39:19 UTC 2021 I: Submitting 8.0K b1/gemma_0.98.4+dfsg-4_arm64.buildinfo.asc Mon Aug 9 14:39:21 UTC 2021 I: Submitting 8.0K b2/gemma_0.98.4+dfsg-4_arm64.buildinfo.asc Mon Aug 9 14:39:23 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Aug 9 14:39:23 UTC 2021 I: Done submitting .buildinfo files. Mon Aug 9 14:39:23 UTC 2021 I: Removing signed gemma_0.98.4+dfsg-4_arm64.buildinfo.asc files: removed './b1/gemma_0.98.4+dfsg-4_arm64.buildinfo.asc' removed './b2/gemma_0.98.4+dfsg-4_arm64.buildinfo.asc'