Sun Jan 26 02:30:10 UTC 2025 I: starting to build gemma/trixie/arm64 on jenkins on '2025-01-26 02:30'
Sun Jan 26 02:30:10 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_6/77004/console.log
Sun Jan 26 02:30:10 UTC 2025 I: Downloading source for trixie/gemma=0.98.5+dfsg-3
--2025-01-26 02:30:11-- http://deb.debian.org/debian/pool/main/g/gemma/gemma_0.98.5%2bdfsg-3.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2125 (2.1K) [text/prs.lines.tag]
Saving to: ‘gemma_0.98.5+dfsg-3.dsc’
0K .. 100% 384M=0s
2025-01-26 02:30:11 (384 MB/s) - ‘gemma_0.98.5+dfsg-3.dsc’ saved [2125/2125]
Sun Jan 26 02:30:11 UTC 2025 I: gemma_0.98.5+dfsg-3.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: gemma
Binary: gemma, gemma-doc
Architecture: any all
Version: 0.98.5+dfsg-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Homepage: https://www.xzlab.org/software.html
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/gemma
Vcs-Git: https://salsa.debian.org/med-team/gemma.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), gfortran, libopenblas-dev, libeigen3-dev, libgsl-dev, zlib1g-dev, catch, shunit2, ruby <!nocheck>
Package-List:
gemma deb science optional arch=any
gemma-doc deb doc optional arch=all
Checksums-Sha1:
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Files:
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f03f4c43ed7fe008187d2fd0dcf6e9c1 6764 gemma_0.98.5+dfsg-3.debian.tar.xz
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Sun Jan 26 02:30:11 UTC 2025 I: Checking whether the package is not for us
Sun Jan 26 02:30:11 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net.
Sun Jan 26 02:30:11 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net.
Sun Jan 26 02:33:56 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Feb 27 20:53:13 -12 2026
I: pbuilder-time-stamp: 1772268793
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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
dpkg-source: warning: cannot verify inline signature for ./gemma_0.98.5+dfsg-3.dsc: unsupported subcommand
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/3370341/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
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 parallel=12 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='840c4c36d9f44bdda6fe9b603c4088f4'
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='3370341'
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/r-b-build.9JvpCdU8/pbuilderrc_FIEQ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9JvpCdU8/b1 --logfile b1/build.log gemma_0.98.5+dfsg-3.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/3370341/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 <pbuilder-maint@lists.alioth.debian.org>
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 ... 19970 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-aarch64-linux-gnu{a} gfortran-aarch64-linux-gnu{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libedit2{a} libeigen3-dev{a} libelf1t64{a} libffi8{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} libunistring5{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, 68 newly installed, 0 to remove and 0 not upgraded.
Need to get 51.7 MB of archives. After unpacking 240 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB]
Get: 3 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB]
Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 5 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 6 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 7 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB]
Get: 8 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 9 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 10 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB]
Get: 11 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 12 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 13 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 14 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB]
Get: 15 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 16 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB]
Get: 18 http://deb.debian.org/debian trixie/main arm64 catch all 1.12.2-0.2 [114 kB]
Get: 19 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB]
Get: 20 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB]
Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 22 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 23 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 24 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 25 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 26 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 27 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 28 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 29 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 30 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB]
Get: 31 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 32 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 33 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB]
Get: 34 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-12 [361 kB]
Get: 35 http://deb.debian.org/debian trixie/main arm64 libgfortran-14-dev arm64 14.2.0-12 [427 kB]
Get: 36 http://deb.debian.org/debian trixie/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-12 [9791 kB]
Get: 37 http://deb.debian.org/debian trixie/main arm64 gfortran-14 arm64 14.2.0-12 [13.4 kB]
Get: 38 http://deb.debian.org/debian trixie/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1 [1284 B]
Get: 39 http://deb.debian.org/debian trixie/main arm64 gfortran arm64 4:14.2.0-1 [1424 B]
Get: 40 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20250104-1 [89.3 kB]
Get: 41 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get: 42 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get: 43 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Get: 44 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB]
Get: 45 http://deb.debian.org/debian trixie/main arm64 libeigen3-dev all 3.4.0-4 [1041 kB]
Get: 46 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB]
Get: 47 http://deb.debian.org/debian trixie/main arm64 libgslcblas0 arm64 2.8+dfsg-5 [84.1 kB]
Get: 48 http://deb.debian.org/debian trixie/main arm64 libgsl28 arm64 2.8+dfsg-5 [881 kB]
Get: 49 http://deb.debian.org/debian trixie/main arm64 libgsl-dev arm64 2.8+dfsg-5 [1118 kB]
Get: 50 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5-2+b1 [96.1 kB]
Get: 51 http://deb.debian.org/debian trixie/main arm64 libopenblas0-pthread arm64 0.3.28+ds-4 [4930 kB]
Get: 52 http://deb.debian.org/debian trixie/main arm64 libopenblas0 arm64 0.3.28+ds-4 [41.0 kB]
Get: 53 http://deb.debian.org/debian trixie/main arm64 libopenblas-pthread-dev arm64 0.3.28+ds-4 [3627 kB]
Get: 54 http://deb.debian.org/debian trixie/main arm64 libopenblas-dev arm64 0.3.28+ds-4 [54.5 kB]
Get: 55 http://deb.debian.org/debian trixie/main arm64 rubygems-integration all 1.19 [5488 B]
Get: 56 http://deb.debian.org/debian trixie/main arm64 ruby3.1 arm64 3.1.2-8.5 [664 kB]
Get: 57 http://deb.debian.org/debian trixie/main arm64 ruby-rubygems all 3.4.20-1 [309 kB]
Get: 58 http://deb.debian.org/debian trixie/main arm64 ruby arm64 1:3.1+support3.3 [5944 B]
Get: 59 http://deb.debian.org/debian trixie/main arm64 rake all 13.2.1-1 [65.2 kB]
Get: 60 http://deb.debian.org/debian trixie/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get: 61 http://deb.debian.org/debian trixie/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB]
Get: 62 http://deb.debian.org/debian trixie/main arm64 ruby-xmlrpc all 0.3.3-2 [24.4 kB]
Get: 63 http://deb.debian.org/debian trixie/main arm64 ruby-sdbm arm64 1.0.0-5+b6 [17.9 kB]
Get: 64 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-2 [49.2 kB]
Get: 65 http://deb.debian.org/debian trixie/main arm64 libruby3.1t64 arm64 3.1.2-8.5 [5267 kB]
Get: 66 http://deb.debian.org/debian trixie/main arm64 libruby arm64 1:3.1+support3.3 [4888 B]
Get: 67 http://deb.debian.org/debian trixie/main arm64 shunit2 all 2.1.8-4 [33.9 kB]
Get: 68 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Fetched 51.7 MB in 0s (188 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
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(Reading database ... 19970 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_3.4.0-2_arm64.deb ...
Unpacking openssl (3.4.0-2) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../02-ca-certificates_20241223_all.deb ...
Unpacking ca-certificates (20241223) ...
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Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:arm64.
Preparing to unpack .../04-libmagic1t64_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ...
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Preparing to unpack .../07-libuchardet0_0.0.8-1+b2_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.8-1+b2) ...
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Unpacking groff-base (1.23.0-7) ...
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Unpacking bsdextrautils (2.40.4-1) ...
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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:arm64 (14.2.0-12) ...
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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
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Setting up ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
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Setting up libopenblas-pthread-dev:arm64 (0.3.28+ds-4) ...
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) ...
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Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
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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:arm64 (0.3.28+ds-4) ...
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Processing triggers for libc-bin (2.40-5) ...
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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: Running cd /build/reproducible-path/gemma-0.98.5+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_0.98.5+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 <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
dh_auto_clean
make -j12 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 -j12 "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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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<double>]',
inlined from 'void ReadFile_cor(const std::string&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<long unsigned int>&, const std::vector<double>&, const std::vector<double>&, const std::map<std::__cxx11::basic_string<char>, long unsigned int>&, const std::map<std::__cxx11::basic_string<char>, long unsigned int>&, const std::map<std::__cxx11::basic_string<char>, double>&, const std::map<std::__cxx11::basic_string<char>, 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<std::__cxx11::basic_string<char> >&, const std::vector<long unsigned int>&, const std::vector<double>&, const std::vector<double>&, const std::map<std::__cxx11::basic_string<char>, long unsigned int>&, const std::map<std::__cxx11::basic_string<char>, long unsigned int>&, const std::map<std::__cxx11::basic_string<char>, double>&, const std::map<std::__cxx11::basic_string<char>, 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 61414
# 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%
**** 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%
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============= 27%
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=============================================== 96%
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================================================== 100%
**** INFO: Done.
GEMMA 0.98.5 (2021-08-25) by Xiang Zhou, Pjotr Prins and team (C) 2012-2021
GSL_RNG_SEED=100
GSL random generator type: mt19937; seed = 100 (option -1); first value = 2333906440
Reading Files ...
**** INFO: no intercept term is found in the cvt file: a column of 1s is added.
## number of total individuals = 198
## number of analyzed individuals = 67
## number of covariates = 3
## number of phenotypes = 1
## number of total SNPs/var = 7320
## number of analyzed SNPs = 7317
Start Eigen-Decomposition...
pve estimate =0.00100086
se(pve) =0.204165
0%
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============= 27%
==================== 41%
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**** 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%
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================ 33%
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================================================== 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%
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============ 25%
================ 33%
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============================ 57%
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======================================== 82%
============================================ 90%
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**** 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%
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================ 33%
==================== 41%
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============================================ 90%
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================================================== 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 ...
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**** 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 = 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
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**** INFO: Done.
.
Finished in 115.447757s, 0.0346 runs/s, 0.1819 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-tHjor2YE
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/0e
objcopy --only-keep-debug --compress-debug-sections debian/gemma/usr/bin/gemma debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/0e/5eae484471a8fcd1a0074b6729608d7378cb90.debug
chmod 0644 -- debian/.debhelper/gemma/dbgsym-root/usr/lib/debug/.build-id/0e/5eae484471a8fcd1a0074b6729608d7378cb90.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/0e/5eae484471a8fcd1a0074b6729608d7378cb90.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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
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=0e5eae484471a8fcd1a0074b6729608d7378cb90 -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 >/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
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-dbgsym' in '../gemma-dbgsym_0.98.5+dfsg-3_arm64.deb'.
dpkg-deb: building package 'gemma' in '../gemma_0.98.5+dfsg-3_arm64.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_arm64.buildinfo
dpkg-genchanges --build=binary -O../gemma_0.98.5+dfsg-3_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/3370341 and its subdirectories
I: Current time: Fri Feb 27 20:56:53 -12 2026
I: pbuilder-time-stamp: 1772269013
Sun Jan 26 02:33:57 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net.
Sun Jan 26 02:33:57 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net.
Sun Jan 26 02:41:08 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net.
Sun Jan 26 02:41:09 UTC 2025 I: gemma_0.98.5+dfsg-3_arm64.changes:
Format: 1.8
Date: Tue, 17 Dec 2024 20:21:45 +0100
Source: gemma
Binary: gemma gemma-dbgsym gemma-doc
Architecture: arm64 all
Version: 0.98.5+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
gemma - Genome-wide Efficient Mixed Model Association
gemma-doc - Example folder for GEMMA
Closes: 1044789
Changes:
gemma (0.98.5+dfsg-3) unstable; urgency=medium
.
* Team upload.
* Fix clean target
Closes: #1044789
* Standards-Version: 4.7.0 (routine-update)
* d/copyright: Update thanks to lrc
Checksums-Sha1:
d1d5a34d58dcc88ab8d0fb9f3696cb69d94a5af8 5556648 gemma-dbgsym_0.98.5+dfsg-3_arm64.deb
fb4c78be2c4bf60cba310197f3d257f6c70e8e77 33411196 gemma-doc_0.98.5+dfsg-3_all.deb
02ba24407e30b18f62a88ecece48ff88526d4ca7 6423 gemma_0.98.5+dfsg-3_arm64.buildinfo
17d90d6b4ffca26b2b245aeed756f143a3aee872 375692 gemma_0.98.5+dfsg-3_arm64.deb
Checksums-Sha256:
17bfb8b78e9877a3b3aa39b0fc694b7d6d9ebd64accf4355101ae991cf16adfb 5556648 gemma-dbgsym_0.98.5+dfsg-3_arm64.deb
aed7f642b372c4f07a88cd9542712cbd5910437847fc81277faf947cfe848724 33411196 gemma-doc_0.98.5+dfsg-3_all.deb
2eecf1861ac1e1fdfee1c6bc49d31113e68a2ef66ec3169988abd4889338aeb1 6423 gemma_0.98.5+dfsg-3_arm64.buildinfo
87607f2d927ab2a9ec034e0b990330aa3c26dba6c4ec0caa5502f2f74b2c07b8 375692 gemma_0.98.5+dfsg-3_arm64.deb
Files:
228f138ff252b7954528ffa5e18d7efa 5556648 debug optional gemma-dbgsym_0.98.5+dfsg-3_arm64.deb
662a826cf2c0a40d6e6f169ed45748d8 33411196 doc optional gemma-doc_0.98.5+dfsg-3_all.deb
72ff697c48f5cbfb50932ad9c24d661d 6423 science optional gemma_0.98.5+dfsg-3_arm64.buildinfo
be7d67da2652cfeb58539ae37790e497 375692 science optional gemma_0.98.5+dfsg-3_arm64.deb
Sun Jan 26 02:41:10 UTC 2025 I: diffoscope 286 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_6-77004.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.9JvpCdU8/gemma_0.98.5+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.9JvpCdU8/gemma_0.98.5+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.9JvpCdU8/gemma_0.98.5+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.9JvpCdU8/b1/gemma_0.98.5+dfsg-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.9JvpCdU8/b2/gemma_0.98.5+dfsg-3_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 diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 229ms
CPU time consumed: 230ms
Sun Jan 26 02:41:14 UTC 2025 I: diffoscope 286 found no differences in the changes files, and a .buildinfo file also exists.
Sun Jan 26 02:41:14 UTC 2025 I: gemma from trixie built successfully and reproducibly on arm64.
Sun Jan 26 02:41:15 UTC 2025 I: Submitting .buildinfo files to external archives:
Sun Jan 26 02:41:15 UTC 2025 I: Submitting 8.0K b1/gemma_0.98.5+dfsg-3_arm64.buildinfo.asc
Sun Jan 26 02:41:16 UTC 2025 I: Submitting 8.0K b2/gemma_0.98.5+dfsg-3_arm64.buildinfo.asc
Sun Jan 26 02:41:17 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Jan 26 02:41:17 UTC 2025 I: Done submitting .buildinfo files.
Sun Jan 26 02:41:17 UTC 2025 I: Removing signed gemma_0.98.5+dfsg-3_arm64.buildinfo.asc files:
removed './b1/gemma_0.98.5+dfsg-3_arm64.buildinfo.asc'
removed './b2/gemma_0.98.5+dfsg-3_arm64.buildinfo.asc'