I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 20 20:31:43 +14 2026 I: pbuilder-time-stamp: 1768890703 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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_0.98.5+dfsg-3.dsc] I: copying [./gemma_0.98.5+dfsg.orig.tar.xz] I: copying [./gemma_0.98.5+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Dec 17 19:32:48 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gemma_0.98.5+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting gemma in gemma-0.98.5+dfsg dpkg-source: info: unpacking gemma_0.98.5+dfsg.orig.tar.xz dpkg-source: info: unpacking gemma_0.98.5+dfsg-3.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 dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/437483/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 20 06:32 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/437483/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/437483/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=289b3d9a824c497ea896d2ace61bdaba LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=437483 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dbBnvkw2/pbuilderrc_CqK9 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dbBnvkw2/b2 --logfile b2/build.log gemma_0.98.5+dfsg-3.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/437483/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: amd64 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, ruby dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 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. pbuilder-satisfydepends-dummy depends on ruby; however: Package ruby 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} ca-certificates{a} catch{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libedit2{a} libeigen3-dev{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libpipeline1{a} libpkgconf3{a} libruby{a} libruby3.1t64{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} rake{a} ruby{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a} shunit2{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx wget zip 0 packages upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 58.2 MB of archives. After unpacking 289 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-3 [200 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-3 [723 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 catch all 1.12.2-0.2 [114 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.21 [88.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-3 [1600 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.21 [919 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-11 [836 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-11 [881 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-11 [11.7 MB] Get: 36 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-11 [13.2 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1 [1284 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:14.2.0-1 [1436 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5-2+b1 [105 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libopenblas0-pthread amd64 0.3.28+ds-4 [6992 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libopenblas0 amd64 0.3.28+ds-4 [41.0 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libopenblas-pthread-dev amd64 0.3.28+ds-4 [4889 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libopenblas-dev amd64 0.3.28+ds-4 [54.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 rubygems-integration all 1.18 [6704 B] Get: 54 http://deb.debian.org/debian unstable/main amd64 ruby3.1 amd64 3.1.2-8.4 [664 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 ruby-rubygems all 3.4.20-1 [309 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 ruby amd64 1:3.1+nmu1 [5584 B] Get: 57 http://deb.debian.org/debian unstable/main amd64 rake all 13.2.1-1 [65.2 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 ruby-xmlrpc all 0.3.3-2 [24.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 ruby-sdbm amd64 1.0.0-5+b5 [15.6 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libruby3.1t64 amd64 3.1.2-8.4 [5411 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libruby amd64 1:3.1+nmu1 [4664 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 shunit2 all 2.1.8-4 [33.9 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Fetched 58.2 MB in 4s (16.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19966 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../01-openssl_3.3.2-2_amd64.deb ... Unpacking openssl (3.3.2-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.22.5-3_amd64.deb ... Unpacking gettext-base (0.22.5-3) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../07-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-6_amd64.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.2-12_amd64.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../10-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.22.5-3_all.deb ... Unpacking autopoint (0.22.5-3) ... Selecting previously unselected package catch. Preparing to unpack .../17-catch_1.12.2-0.2_all.deb ... Unpacking catch (1.12.2-0.2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.21_all.deb ... Unpacking libdebhelper-perl (13.21) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../24-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../26-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.22.5-3_amd64.deb ... Unpacking gettext (0.22.5-3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.21_all.deb ... Unpacking debhelper (13.21) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../32-libgfortran5_14.2.0-11_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-11) ... Selecting previously unselected package libgfortran-14-dev:amd64. Preparing to unpack .../33-libgfortran-14-dev_14.2.0-11_amd64.deb ... Unpacking libgfortran-14-dev:amd64 (14.2.0-11) ... Selecting previously unselected package gfortran-14-x86-64-linux-gnu. Preparing to unpack .../34-gfortran-14-x86-64-linux-gnu_14.2.0-11_amd64.deb ... Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-11) ... Selecting previously unselected package gfortran-14. Preparing to unpack .../35-gfortran-14_14.2.0-11_amd64.deb ... Unpacking gfortran-14 (14.2.0-11) ... Selecting previously unselected package gfortran-x86-64-linux-gnu. Preparing to unpack .../36-gfortran-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb ... Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1) ... Selecting previously unselected package gfortran. Preparing to unpack .../37-gfortran_4%3a14.2.0-1_amd64.deb ... Unpacking gfortran (4:14.2.0-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../38-libedit2_3.1-20240808-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240808-1) ... Selecting previously unselected package libpkgconf3:amd64. 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Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libncurses6:amd64 (6.5-2+b1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up autopoint (0.22.5-3) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libgfortran5:amd64 (14.2.0-11) ... Setting up autoconf (2.72-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up catch (1.12.2-0.2) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up openssl (3.3.2-2) ... Setting up ruby-xmlrpc (0.3.3-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... 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 libgfortran-14-dev:amd64 (14.2.0-11) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-3) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libopenblas0-pthread:amd64 (0.3.28+ds-4) ... 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 (2.4.7-8) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-11) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libeigen3-dev (3.4.0-4) ... Setting up pkg-config:amd64 (1.8.1-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libopenblas0:amd64 (0.3.28+ds-4) ... Setting up groff-base (1.23.0-6) ... Setting up gfortran-14 (14.2.0-11) ... Setting up libopenblas-pthread-dev:amd64 (0.3.28+ds-4) ... 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 rubygems-integration (1.18) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1) ... Setting up gfortran (4:14.2.0-1) ... 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 libopenblas-dev:amd64 (0.3.28+ds-4) ... Setting up debhelper (13.21) ... Setting up ruby3.1 (3.1.2-8.4) ... Setting up libruby3.1t64:amd64 (3.1.2-8.4) ... Setting up libruby:amd64 (1:3.1+nmu1) ... Setting up ruby (1:3.1+nmu1) ... Setting up rake (13.2.1-1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b5) ... Setting up ruby-rubygems (3.4.20-1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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: user script /srv/workspace/pbuilder/437483/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/437483/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/gemma-0.98.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../gemma_0.98.5+dfsg-3_source.changes dpkg-buildpackage: info: source package gemma dpkg-buildpackage: info: source version 0.98.5+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j42 clean make[1]: Entering directory '/build/reproducible-path/gemma-0.98.5+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/reproducible-path/gemma-0.98.5+dfsg' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/gemma-0.98.5+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 \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) rm -f *.log rm -rf test/output/ rm -f bin/gemma make[1]: Leaving directory '/build/reproducible-path/gemma-0.98.5+dfsg' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j42 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/gemma-0.98.5+dfsg' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 In file included from /usr/include/c++/14/vector:66, from src/vc.cpp:33: In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ReadFile_cor(const std::string&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::map, long unsigned int>&, const std::map, long unsigned int>&, const std::map, double>&, const std::map, long unsigned int>&, size_t, const double&, const double&, const double&, gsl_matrix*, gsl_matrix*, gsl_vector*, size_t&, size_t&, size_t&, size_t&)' at src/vc.cpp:1200:37: /usr/include/c++/14/bits/stl_vector.h:1131:41: warning: 'bin' may be used uninitialized [-Wmaybe-uninitialized] 1131 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ src/vc.cpp: In function 'void ReadFile_cor(const std::string&, const std::vector >&, const std::vector&, const std::vector&, const std::vector&, const std::map, long unsigned int>&, const std::map, long unsigned int>&, const std::map, double>&, const std::map, long unsigned int>&, size_t, const double&, const double&, const double&, gsl_matrix*, gsl_matrix*, gsl_vector*, size_t&, size_t&, size_t&, size_t&)': src/vc.cpp:1024:52: note: 'bin' was declared here 1024 | size_t n_nb, nsamp1, nsamp2, n12, bin_size = 10, bin; | ^~~ 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,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/reproducible-path/gemma-0.98.5+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/gemma-0.98.5+dfsg' dh_auto_test --no-parallel make -j1 check make[2]: Entering directory '/build/reproducible-path/gemma-0.98.5+dfsg' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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=/build/reproducible-path/gemma-0.98.5+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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,-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 47924 # Running: GSL_RNG_SEED=100 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins 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% Mismatch coordinates (194,0)0:0! **** WARNING: 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. GSL_RNG_SEED=100 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins 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. .GSL_RNG_SEED=100 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins 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% Mismatch coordinates (4,0)0:0! **** WARNING: K is not symmetric! in src/gemma.cpp at line 1913 in BatchRun **** INFO: Done. GSL_RNG_SEED=100 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins 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. .GSL_RNG_SEED=100 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 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% 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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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================================================= 99% ================================================= 99% ================================================= 100% ================================================= 100% ================================================== 100% **** INFO: Done. .GSL_RNG_SEED=100 GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021 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. . Finished in 121.705989s, 0.0329 runs/s, 0.1725 assertions/s. 4 runs, 21 assertions, 0 failures, 0 errors, 0 skips make[2]: Leaving directory '/build/reproducible-path/gemma-0.98.5+dfsg' rm -fr -- /tmp/dh-xdg-rundir-sgY3yCVz rm -rf output make[1]: Leaving directory '/build/reproducible-path/gemma-0.98.5+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 -m0755 -d /build/reproducible-path/gemma-0.98.5\+dfsg/debian/tmp dh_install install -m0755 -d debian/gemma/usr/bin cp --reflink=auto -a ./bin/gemma debian/gemma/usr/bin/ dh_installdocs install -m0755 -d debian/gemma/usr/share/doc/gemma install -m0755 -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 -m0755 -d debian/gemma-doc/usr/share/doc/gemma-doc install -m0755 -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/reproducible-path/gemma-0.98.5+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 -m0755 -d debian/gemma-doc/usr/share/doc/gemma-doc install -p -m0644 debian/.debhelper/generated/gemma-doc/dh_installchangelogs.dch.trimmed debian/gemma-doc/usr/share/doc/gemma-doc/changelog.Debian install -m0755 -d debian/gemma/usr/share/doc/gemma install -p -m0644 debian/.debhelper/generated/gemma/dh_installchangelogs.dch.trimmed debian/gemma/usr/share/doc/gemma/changelog.Debian dh_perl dh_link dh_strip_nondeterminism Using 1734463305 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/README.md usr/share/doc/gemma/RELEASE-NOTES.md usr/share/doc/gemma/changelog.Debian 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 cd '/build/reproducible-path/gemma-0.98.5+dfsg' cd '/build/reproducible-path/gemma-0.98.5+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-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 find debian/gemma/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a dwz -- debian/gemma/usr/bin/gemma dh_strip -a install -m0755 -d debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/69 objcopy --only-keep-debug --compress-debug-sections debian/gemma/usr/bin/gemma debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/69/4eb0c58a7adb3bfb0d9aa6ee50b7f6cea9f07d.debug chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/69/4eb0c58a7adb3bfb0d9aa6ee50b7f6cea9f07d.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/69/4eb0c58a7adb3bfb0d9aa6ee50b7f6cea9f07d.debug debian/gemma/usr/bin/gemma install -m0755 -d debian/.debhelper/gemma/dbgsym-root/usr/share/doc ln -s gemma debian/.debhelper/gemma/dbgsym-root/usr/share/doc/gemma-dbgsym install -m0755 -d debian/.debhelper/gemma dh_makeshlibs -a rm -f debian/gemma/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/gemma/DEBIAN dpkg-shlibdeps -Tdebian/gemma.substvars debian/gemma/usr/bin/gemma dh_installdeb install -m0755 -d debian/gemma/DEBIAN install -m0755 -d debian/gemma-doc/DEBIAN dh_gencontrol install -m0755 -d debian/gemma-doc/DEBIAN 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 -cdebian/control -Pdebian/gemma-doc install -m0755 -d debian/gemma/DEBIAN echo misc:Depends= >> debian/gemma.substvars echo misc:Pre-Depends= >> debian/gemma.substvars install -m0755 -d debian/.debhelper/gemma/dbgsym-root/DEBIAN dpkg-gencontrol -pgemma -ldebian/changelog -Tdebian/gemma.substvars -cdebian/control -Pdebian/.debhelper/gemma/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=gemma-dbgsym "-DDepends=gemma (= \${binary:Version})" "-DDescription=debug symbols for gemma" -DBuild-Ids=694eb0c58a7adb3bfb0d9aa6ee50b7f6cea9f07d -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 -cdebian/control -Pdebian/gemma chmod 0644 -- debian/gemma/DEBIAN/control dh_md5sums install -m0755 -d debian/gemma/DEBIAN install -m0755 -d debian/gemma-doc/DEBIAN cd debian/gemma-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/gemma >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/gemma/DEBIAN/md5sums install -m0755 -d debian/.debhelper/gemma/dbgsym-root/DEBIAN 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 --root-owner-group --build debian/gemma-doc .. dpkg-deb: building package 'gemma' in '../gemma_0.98.5+dfsg-3_amd64.deb'. dpkg-deb: building package 'gemma-dbgsym' in '../gemma-dbgsym_0.98.5+dfsg-3_amd64.deb'. dpkg-deb: building package 'gemma-doc' in '../gemma-doc_0.98.5+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../gemma_0.98.5+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../gemma_0.98.5+dfsg-3_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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/437483/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/437483/tmp/hooks/B01_cleanup finished 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/437483 and its subdirectories I: Current time: Tue Jan 20 20:36:56 +14 2026 I: pbuilder-time-stamp: 1768891016