Sat Feb 22 15:19:34 UTC 2025 I: starting to build fastqtl/trixie/i386 on jenkins on '2025-02-22 15:19'
Sat Feb 22 15:19:34 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_6/56223/console.log
Sat Feb 22 15:19:34 UTC 2025 I: Downloading source for trixie/fastqtl=2.184+v7+dfsg-4
--2025-02-22 15:19:34-- http://deb.debian.org/debian/pool/main/f/fastqtl/fastqtl_2.184%2bv7%2bdfsg-4.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2406 (2.3K) [text/prs.lines.tag]
Saving to: ‘fastqtl_2.184+v7+dfsg-4.dsc’
0K .. 100% 355M=0s
2025-02-22 15:19:34 (355 MB/s) - ‘fastqtl_2.184+v7+dfsg-4.dsc’ saved [2406/2406]
Sat Feb 22 15:19:34 UTC 2025 I: fastqtl_2.184+v7+dfsg-4.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: fastqtl
Binary: fastqtl, fastqtl-doc
Architecture: any all
Version: 2.184+v7+dfsg-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Dylan Aïssi <daissi@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: http://fastqtl.sourceforge.net/
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/fastqtl
Vcs-Git: https://salsa.debian.org/med-team/fastqtl.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), dh-python, python3, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libgsl-dev, r-mathlib, zlib1g-dev, libblas-dev, libeigen3-dev, libhts-dev, libbz2-dev
Package-List:
fastqtl deb science optional arch=any
fastqtl-doc deb doc optional arch=all
Checksums-Sha1:
afda0774d21c6c870b5bf319751f46a641d1dd12 17128664 fastqtl_2.184+v7+dfsg.orig.tar.xz
5b737b2493b7569eb93b82fed1a81ccd584009c9 20936 fastqtl_2.184+v7+dfsg-4.debian.tar.xz
Checksums-Sha256:
a16310e5cc00873707decb7dad8acd9d5ae22bf4ade1fdbba3a99afc650a6232 17128664 fastqtl_2.184+v7+dfsg.orig.tar.xz
4ad54980be7c13f24cdd856456542c1b0947a328b92a127ff9c91313b4085ea6 20936 fastqtl_2.184+v7+dfsg-4.debian.tar.xz
Files:
0315c13229da6648d451f9025370a919 17128664 fastqtl_2.184+v7+dfsg.orig.tar.xz
8b6d3ab4b8e1e56f2e9dedd79964300a 20936 fastqtl_2.184+v7+dfsg-4.debian.tar.xz
Dgit: 1b9cf93248bc5bf8fa33ef1d00f928a70726fe89 debian archive/debian/2.184+v7+dfsg-4 https://git.dgit.debian.org/fastqtl
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Sat Feb 22 15:19:34 UTC 2025 I: Checking whether the package is not for us
Sat Feb 22 15:19:34 UTC 2025 I: Starting 1st build on remote node ionos6-i386.debian.net.
Sat Feb 22 15:19:34 UTC 2025 I: Preparing to do remote build '1' on ionos6-i386.debian.net.
Sat Feb 22 15:21:00 UTC 2025 I: Deleting $TMPDIR on ionos6-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Mar 27 09:42:38 -12 2026
I: pbuilder-time-stamp: 1774647758
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: using eatmydata during job
I: Copying source file
I: copying [fastqtl_2.184+v7+dfsg-4.dsc]
I: copying [./fastqtl_2.184+v7+dfsg.orig.tar.xz]
I: copying [./fastqtl_2.184+v7+dfsg-4.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./fastqtl_2.184+v7+dfsg-4.dsc: unsupported subcommand
dpkg-source: info: extracting fastqtl in fastqtl-2.184+v7+dfsg
dpkg-source: info: unpacking fastqtl_2.184+v7+dfsg.orig.tar.xz
dpkg-source: info: unpacking fastqtl_2.184+v7+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 01_Makefile_dynamic_hardenings.patch
dpkg-source: info: applying 02_Replace_libtabix_by_libhts.patch
dpkg-source: info: applying 03_Reproducible_builds.patch
dpkg-source: info: applying cross.patch
dpkg-source: info: applying set_path.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/103323/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='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='64847e1f8426448a90fa917944c21145'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='103323'
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.Y6S2OnGA/pbuilderrc_YZfg --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.Y6S2OnGA/b1 --logfile b1/build.log fastqtl_2.184+v7+dfsg-4.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos6-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) 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/103323/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: i386
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), dh-python, python3, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libgsl-dev, r-mathlib, zlib1g-dev, libblas-dev, libeigen3-dev, libhts-dev, libbz2-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19844 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 dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on libboost-dev; however:
Package libboost-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however:
Package libboost-iostreams-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however:
Package libboost-program-options-dev is not installed.
pbuilder-satisfydepends-dummy depends on libgsl-dev; however:
Package libgsl-dev is not installed.
pbuilder-satisfydepends-dummy depends on r-mathlib; however:
Package r-mathlib is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libblas-dev; however:
Package libblas-dev is not installed.
pbuilder-satisfydepends-dummy depends on libeigen3-dev; however:
Package libeigen3-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev; however:
Package libhts-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
Package libbz2-dev 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} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libeigen3-dev{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} r-mathlib{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix r-base-core r-base-dev wget
0 packages upgraded, 138 newly installed, 0 to remove and 0 not upgraded.
Need to get 78.1 MB of archives. After unpacking 417 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.13-minimal i386 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 python3.13-minimal i386 3.13.2-1 [2266 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.13.1-2 [27.0 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 libffi8 i386 3.4.7-1 [21.4 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 libpython3.13-stdlib i386 3.13.2-1 [1985 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 python3.13 i386 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.13.1-2 [9952 B]
Get: 14 http://deb.debian.org/debian trixie/main i386 python3 i386 3.13.1-2 [28.0 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-3 [96.2 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 comerr-dev i386 2.1-1.47.2-1 [56.2 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 38 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 41 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 48 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 50 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 51 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 53 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 56 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 57 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 75.6.0-1 [720 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20250108 [113 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 icu-devtools i386 72.1-6 [218 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB]
Get: 61 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 63 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-4 [354 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 libgssrpc4t64 i386 1.21.3-4 [63.4 kB]
Get: 66 http://deb.debian.org/debian trixie/main i386 libkadm5clnt-mit12 i386 1.21.3-4 [44.1 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 libkdb5-10t64 i386 1.21.3-4 [45.3 kB]
Get: 68 http://deb.debian.org/debian trixie/main i386 libkadm5srv-mit12 i386 1.21.3-4 [57.7 kB]
Get: 69 http://deb.debian.org/debian trixie/main i386 krb5-multidev i386 1.21.3-4 [126 kB]
Get: 70 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.1-2 [150 kB]
Get: 71 http://deb.debian.org/debian trixie/main i386 libblas-dev i386 3.12.1-2 [162 kB]
Get: 72 http://deb.debian.org/debian trixie/main i386 libboost1.83-dev i386 1.83.0-4.1 [10.6 MB]
Get: 73 http://deb.debian.org/debian trixie/main i386 libboost-dev i386 1.83.0.2+b2 [3840 B]
Get: 74 http://deb.debian.org/debian trixie/main i386 libboost-regex1.83.0 i386 1.83.0-4.1 [329 kB]
Get: 75 http://deb.debian.org/debian trixie/main i386 libicu-dev i386 72.1-6 [10.6 MB]
Get: 76 http://deb.debian.org/debian trixie/main i386 libboost-regex1.83-dev i386 1.83.0-4.1 [347 kB]
Get: 77 http://deb.debian.org/debian trixie/main i386 libboost-iostreams1.83-dev i386 1.83.0-4.1 [264 kB]
Get: 78 http://deb.debian.org/debian trixie/main i386 libboost-iostreams-dev i386 1.83.0.2+b2 [3588 B]
Get: 79 http://deb.debian.org/debian trixie/main i386 libboost-program-options1.83.0 i386 1.83.0-4.1 [361 kB]
Get: 80 http://deb.debian.org/debian trixie/main i386 libboost-program-options1.83-dev i386 1.83.0-4.1 [390 kB]
Get: 81 http://deb.debian.org/debian trixie/main i386 libboost-program-options-dev i386 1.83.0.2+b2 [3616 B]
Get: 82 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 83 http://deb.debian.org/debian trixie/main i386 libbrotli-dev i386 1.1.0-2+b6 [313 kB]
Get: 84 http://deb.debian.org/debian trixie/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB]
Get: 85 http://deb.debian.org/debian trixie/main i386 libidn2-0 i386 2.3.7-2+b1 [130 kB]
Get: 86 http://deb.debian.org/debian trixie/main i386 libp11-kit0 i386 0.25.5-3 [423 kB]
Get: 87 http://deb.debian.org/debian trixie/main i386 libtasn1-6 i386 4.20.0-2 [51.6 kB]
Get: 88 http://deb.debian.org/debian trixie/main i386 libgnutls30t64 i386 3.8.9-2 [1462 kB]
Get: 89 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8+b1 [20.9 kB]
Get: 90 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8+b1 [61.3 kB]
Get: 91 http://deb.debian.org/debian trixie/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB]
Get: 92 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 93 http://deb.debian.org/debian trixie/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB]
Get: 94 http://deb.debian.org/debian trixie/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB]
Get: 95 http://deb.debian.org/debian trixie/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB]
Get: 96 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 97 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 98 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 99 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.12.1-2 [411 kB]
Get: 100 http://deb.debian.org/debian trixie/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB]
Get: 101 http://deb.debian.org/debian trixie/main i386 libunbound8 i386 1.22.0-1+b1 [633 kB]
Get: 102 http://deb.debian.org/debian trixie/main i386 libgnutls-dane0t64 i386 3.8.9-2 [453 kB]
Get: 103 http://deb.debian.org/debian trixie/main i386 libgnutls-openssl27t64 i386 3.8.9-2 [453 kB]
Get: 104 http://deb.debian.org/debian trixie/main i386 libidn2-dev i386 2.3.7-2+b1 [126 kB]
Get: 105 http://deb.debian.org/debian trixie/main i386 libp11-kit-dev i386 0.25.5-3 [208 kB]
Get: 106 http://deb.debian.org/debian trixie/main i386 libtasn1-6-dev i386 4.20.0-2 [103 kB]
Get: 107 http://deb.debian.org/debian trixie/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-3 [329 kB]
Get: 108 http://deb.debian.org/debian trixie/main i386 libgmp-dev i386 2:6.3.0+dfsg-3 [661 kB]
Get: 109 http://deb.debian.org/debian trixie/main i386 nettle-dev i386 3.10-1+b1 [1334 kB]
Get: 110 http://deb.debian.org/debian trixie/main i386 libgnutls28-dev i386 3.8.9-2 [1464 kB]
Get: 111 http://deb.debian.org/debian trixie/main i386 libkrb5-dev i386 1.21.3-4 [15.9 kB]
Get: 112 http://deb.debian.org/debian trixie/main i386 libldap-dev i386 2.6.9+dfsg-1 [328 kB]
Get: 113 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB]
Get: 114 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB]
Get: 115 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB]
Get: 116 http://deb.debian.org/debian trixie/main i386 libnghttp2-dev i386 1.64.0-1 [123 kB]
Get: 117 http://deb.debian.org/debian trixie/main i386 libnghttp3-dev i386 1.6.0-2 [101 kB]
Get: 118 http://deb.debian.org/debian trixie/main i386 libngtcp2-crypto-gnutls-dev i386 1.9.1-1 [24.0 kB]
Get: 119 http://deb.debian.org/debian trixie/main i386 libngtcp2-dev i386 1.9.1-1 [202 kB]
Get: 120 http://deb.debian.org/debian trixie/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB]
Get: 121 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 122 http://deb.debian.org/debian trixie/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-2+b5 [72.3 kB]
Get: 123 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.4.1-1 [2837 kB]
Get: 124 http://deb.debian.org/debian trixie/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB]
Get: 125 http://deb.debian.org/debian trixie/main i386 libzstd-dev i386 1.5.6+dfsg-2 [354 kB]
Get: 126 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.12.1-2 [542 kB]
Get: 127 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.23-1+b1 [48.4 kB]
Get: 128 http://deb.debian.org/debian trixie/main i386 libdeflate-dev i386 1.23-1+b1 [57.5 kB]
Get: 129 http://deb.debian.org/debian trixie/main i386 pkg-config i386 1.8.1-4 [14.0 kB]
Get: 130 http://deb.debian.org/debian trixie/main i386 libeigen3-dev all 3.4.0-4 [1041 kB]
Get: 131 http://deb.debian.org/debian trixie/main i386 libgslcblas0 i386 2.8+dfsg-5 [106 kB]
Get: 132 http://deb.debian.org/debian trixie/main i386 libgsl28 i386 2.8+dfsg-5 [978 kB]
Get: 133 http://deb.debian.org/debian trixie/main i386 libgsl-dev i386 2.8+dfsg-5 [1240 kB]
Get: 134 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.1-2 [70.9 kB]
Get: 135 http://deb.debian.org/debian trixie/main i386 libhts3t64 i386 1.21+ds-1 [506 kB]
Get: 136 http://deb.debian.org/debian trixie/main i386 liblzma-dev i386 5.6.3-1+b1 [328 kB]
Get: 137 http://deb.debian.org/debian trixie/main i386 libhts-dev i386 1.21+ds-1 [1725 kB]
Get: 138 http://deb.debian.org/debian trixie/main i386 r-mathlib i386 4.4.2-1 [2598 kB]
Fetched 78.1 MB in 1s (87.1 MB/s)
Preconfiguring packages ...
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Unpacking libpython3.13-minimal:i386 (3.13.2-1) ...
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Unpacking libexpat1:i386 (2.6.4-1) ...
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Setting up libpython3.13-minimal:i386 (3.13.2-1) ...
Setting up libexpat1:i386 (2.6.4-1) ...
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Selecting previously unselected package python3-minimal.
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Unpacking python3-minimal (3.13.1-2) ...
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Unpacking tzdata (2025a-2) ...
Selecting previously unselected package libffi8:i386.
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Unpacking libffi8:i386 (3.4.7-1) ...
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Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:i386.
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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:i386 (8.2-6) ...
Selecting previously unselected package libpython3.13-stdlib:i386.
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Unpacking libpython3.13-stdlib:i386 (3.13.2-1) ...
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Setting up python3-minimal (3.13.1-2) ...
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Preparing to unpack .../000-python3_3.13.1-2_i386.deb ...
Unpacking python3 (3.13.1-2) ...
Selecting previously unselected package sensible-utils.
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Unpacking gettext-base (0.23.1-1) ...
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Unpacking libk5crypto3:i386 (1.21.3-4) ...
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Unpacking libkeyutils1:i386 (1.6.3-4) ...
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Setting up libpython3-stdlib:i386 (3.13.1-2) ...
Setting up libgnutls30t64:i386 (3.8.9-2) ...
Setting up libgnutls-openssl27t64:i386 (3.8.9-2) ...
Setting up libnghttp2-dev:i386 (1.64.0-1) ...
Setting up python3.13 (3.13.2-1) ...
Setting up libboost-iostreams1.83-dev:i386 (1.83.0-4.1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpsl5t64:i386 (0.21.2-1.1+b1) ...
Setting up python3 (3.13.1-2) ...
Setting up libboost-iostreams-dev:i386 (1.83.0.2+b2) ...
Setting up python3-zipp (3.21.0-1) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpsl-dev:i386 (0.21.2-1.1+b1) ...
Setting up libgnutls-dane0t64:i386 (3.8.9-2) ...
Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libgssrpc4t64:i386 (1.21.3-4) ...
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Setting up libkadm5clnt-mit12:i386 (1.21.3-4) ...
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Setting up python3-jaraco.context (6.0.0-1) ...
Setting up libkdb5-10t64:i386 (1.21.3-4) ...
Setting up python3-typeguard (4.4.1-1) ...
Setting up libcurl3t64-gnutls:i386 (8.12.1-2) ...
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Setting up python3-inflect (7.3.1-2) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up librtmp-dev:i386 (2.4+20151223.gitfa8646d.1-2+b5) ...
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Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/fastqtl-2.184+v7+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 > ../fastqtl_2.184+v7+dfsg-4_source.changes
dpkg-buildpackage: info: source package fastqtl
dpkg-buildpackage: info: source version 2.184+v7+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --with python3
dh_auto_clean
make -j22 clean
make[1]: Entering directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg'
rm -f obj/*.o bin/fastQTL
make[1]: Leaving directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg'
dh_clean
debian/rules binary
dh binary --with python3
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg'
mkdir -p /build/reproducible-path/fastqtl-2.184+v7+dfsg/obj/
mkdir -p /build/reproducible-path/fastqtl-2.184+v7+dfsg/bin/
dh_auto_build -- CXXFLAGS='-g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14'
make -j22 "INSTALL=install --strip-program=true" "CXXFLAGS=-g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14"
make[2]: Entering directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg'
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisMapping.o -c src/analysisMapping.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisNominal.o -c src/analysisNominal.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisNominalBest.o -c src/analysisNominalBest.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutation.o -c src/analysisPermutation.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationInteraction.o -c src/analysisPermutationInteraction.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationPerGroup.o -c src/analysisPermutationPerGroup.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationSequence.o -c src/analysisPermutationSequence.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/commands.o -c src/commands.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/df.o -c src/df.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/fastQTL.o -c src/fastQTL.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/management.o -c src/management.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/mle.o -c src/mle.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readCovariates.o -c src/readCovariates.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGenotypes.o -c src/readGenotypes.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGroups.o -c src/readGroups.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInclusionsExclusions.o -c src/readInclusionsExclusions.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInteractions.o -c src/readInteractions.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readPhenotypes.o -c src/readPhenotypes.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readThresholds.o -c src/readThresholds.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/residualizer.o -c src/residualizer.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/tabix.o -c src/utils/tabix.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/reproducible-path/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/utils.o -c src/utils/utils.cpp -Isrc
src/utils/tabix.cpp: In constructor 'Tabix::Tabix(std::string&)':
src/utils/tabix.cpp:17:22: warning: 'int bgzf_is_bgzf(const char*)' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
17 | if ( bgzf_is_bgzf(cfilename)!=1 )
| ~~~~~~~~~~~~^~~~~~~~~~~
In file included from src/utils/tabix.hpp:12,
from src/utils/tabix.cpp:6:
/usr/include/htslib/bgzf.h:309:9: note: declared here
309 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
| ^~~~~~~~~~~~
src/utils/utils.cpp: In function 'void putils::random_shuffle(std::vector<std::vector<float> >&)':
src/utils/utils.cpp:133:31: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<int*, vector<int> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
133 | random_shuffle(O.begin(), O.end());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/algorithm:61,
from src/utils/utils.h:54,
from src/utils/utils.cpp:17:
/usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here
4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
| ^~~~~~~~~~~~~~
src/analysisPermutation.cpp: In member function 'void data::runPermutation(std::string, std::vector<int>)':
src/analysisPermutation.cpp:75:27: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<float*, vector<float> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
75 | random_shuffle(phenotype_curr.begin(), phenotype_curr.end());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/algorithm:61,
from src/utils/utils.h:54,
from src/data.h:25,
from src/analysisPermutation.cpp:17:
/usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here
4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
| ^~~~~~~~~~~~~~
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisNominal.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
src/analysisPermutationInteraction.cpp: In member function 'void data::runPermutationInteraction(std::string, int)':
src/analysisPermutationInteraction.cpp:48:39: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<float*, vector<float> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
48 | random_shuffle(permuted_phenotypes[perm].begin(), permuted_phenotypes[perm].end());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/algorithm:61,
from src/utils/utils.h:54,
from src/data.h:25,
from src/analysisPermutationInteraction.cpp:17:
/usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here
4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
| ^~~~~~~~~~~~~~
src/analysisPermutationInteraction.cpp:76:47: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<float*, vector<float> >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
76 | random_shuffle(phenotype_curr.begin(), phenotype_curr.end());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here
4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
| ^~~~~~~~~~~~~~
In file included from src/analysisPermutationPerGroup.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisPermutationSequence.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisNominalBest.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/management.cpp:20:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisMapping.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++11 -O3 -Wl,-z,relro -Wl,-z,now obj/analysisMapping.o obj/analysisNominal.o obj/analysisNominalBest.o obj/analysisPermutation.o obj/analysisPermutationInteraction.o obj/analysisPermutationPerGroup.o obj/analysisPermutationSequence.o obj/commands.o obj/df.o obj/fastQTL.o obj/management.o obj/mle.o obj/readCovariates.o obj/readGenotypes.o obj/readGroups.o obj/readInclusionsExclusions.o obj/readInteractions.o obj/readPhenotypes.o obj/readThresholds.o obj/residualizer.o obj/tabix.o obj/utils.o -lRmath -lhts -lm -lz -lbz2 -lboost_iostreams -lboost_program_options -lgslcblas -lgsl -lblas -o bin/fastQTL
make[2]: Leaving directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg'
cd /build/reproducible-path/fastqtl-2.184+v7+dfsg/example/ && \
tar Jcvf examples.tar.xz * --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner
covariates.txt.gz
genotypes.vcf.gz
genotypes.vcf.gz.tbi
interaction.txt
phenotypes.bed.gz
phenotypes.bed.gz.tbi
make[1]: Leaving directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg'
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
dh_install
dh_installdocs
dh_installchangelogs
dh_installman
dh_python3
I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/run_chunk.py
I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/run_FastQTL_threaded.py
I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/annotate_outputs.py
I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/sort_index_pairs.py
I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/merge_chunks.py
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
debian/rules execute_after_dh_fixperms-arch
make[1]: Entering directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg'
chmod -x debian/*/usr/share/fastqtl/*.R
make[1]: Leaving directory '/build/reproducible-path/fastqtl-2.184+v7+dfsg'
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/fastqtl/usr/bin/fastQTL was not linked against libblas.so.3 (it uses none of the library's symbols)
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'fastqtl-dbgsym' in '../fastqtl-dbgsym_2.184+v7+dfsg-4_i386.deb'.
dpkg-deb: building package 'fastqtl-doc' in '../fastqtl-doc_2.184+v7+dfsg-4_all.deb'.
dpkg-deb: building package 'fastqtl' in '../fastqtl_2.184+v7+dfsg-4_i386.deb'.
dpkg-genbuildinfo --build=binary -O../fastqtl_2.184+v7+dfsg-4_i386.buildinfo
dpkg-genchanges --build=binary -O../fastqtl_2.184+v7+dfsg-4_i386.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/103323 and its subdirectories
I: Current time: Fri Mar 27 09:43:58 -12 2026
I: pbuilder-time-stamp: 1774647838
Sat Feb 22 15:21:01 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net.
Sat Feb 22 15:21:01 UTC 2025 I: Preparing to do remote build '2' on ionos12-i386.debian.net.
Sat Feb 22 15:23:14 UTC 2025 I: Deleting $TMPDIR on ionos12-i386.debian.net.
Sat Feb 22 15:23:14 UTC 2025 I: fastqtl_2.184+v7+dfsg-4_i386.changes:
Format: 1.8
Date: Fri, 15 Dec 2023 19:31:08 +0100
Source: fastqtl
Binary: fastqtl fastqtl-dbgsym fastqtl-doc
Architecture: i386 all
Version: 2.184+v7+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
fastqtl - Quantitative Trait Loci (QTL) mapper in cis for molecular phenoty
fastqtl-doc - QTL mapper in cis for molecular phenotypes - documentation
Closes: 1044949 1049574
Changes:
fastqtl (2.184+v7+dfsg-4) unstable; urgency=medium
.
* d/control: add myself to uploaders.
* d/control: remove redundant ${misc:Depends}.
* d/clean: new: remove leftover artifact. (Closes: #1044949, #1049574)
Checksums-Sha1:
9b1b85eef4ee674bf20c50a05b709e1fe12546ef 5254704 fastqtl-dbgsym_2.184+v7+dfsg-4_i386.deb
6ceb567088089b39c73a84721f541be9997971b2 17104880 fastqtl-doc_2.184+v7+dfsg-4_all.deb
f6f258dfc6991aa74d89c155dc207d1ff84608ad 8705 fastqtl_2.184+v7+dfsg-4_i386.buildinfo
7c1f818d8d02524eee49d6549cd12e706d287466 240120 fastqtl_2.184+v7+dfsg-4_i386.deb
Checksums-Sha256:
ae31340f123182e9a57015f13261e4d9503b79981701278622e5598cbd52e877 5254704 fastqtl-dbgsym_2.184+v7+dfsg-4_i386.deb
73ac428d986ddad41814615e1bcaf434da16b4969c536c6bf6a4e8257e6f6e78 17104880 fastqtl-doc_2.184+v7+dfsg-4_all.deb
58fc4eba073f7885d52254203d7e825f66fad30a12d8ae7de8ef35f56225ac22 8705 fastqtl_2.184+v7+dfsg-4_i386.buildinfo
638c9c37a7428bd7c81092c133a68a34ac0febf1a32e9480a95feac5c640da97 240120 fastqtl_2.184+v7+dfsg-4_i386.deb
Files:
809d09d103d39e03c62f2c7d8eecb2f9 5254704 debug optional fastqtl-dbgsym_2.184+v7+dfsg-4_i386.deb
1b19cf583cbcce1588212b6a6f54a226 17104880 doc optional fastqtl-doc_2.184+v7+dfsg-4_all.deb
ff5056a8c8dde42b2f3f08a95c2a076c 8705 science optional fastqtl_2.184+v7+dfsg-4_i386.buildinfo
4a4dea2dad5b281933d60f36f9558f8e 240120 science optional fastqtl_2.184+v7+dfsg-4_i386.deb
Sat Feb 22 15:23:15 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-i386_6-56223.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/fastqtl_2.184+v7+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/fastqtl_2.184+v7+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/fastqtl_2.184+v7+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/b1/fastqtl_2.184+v7+dfsg-4_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/b2/fastqtl_2.184+v7+dfsg-4_i386.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: 240ms
CPU time consumed: 239ms
Sat Feb 22 15:23:16 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Sat Feb 22 15:23:16 UTC 2025 I: fastqtl from trixie built successfully and reproducibly on i386.
Sat Feb 22 15:23:17 UTC 2025 I: Submitting .buildinfo files to external archives:
Sat Feb 22 15:23:17 UTC 2025 I: Submitting 12K b1/fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc
Sat Feb 22 15:23:19 UTC 2025 I: Submitting 12K b2/fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc
Sat Feb 22 15:23:20 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Feb 22 15:23:20 UTC 2025 I: Done submitting .buildinfo files.
Sat Feb 22 15:23:20 UTC 2025 I: Removing signed fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc files:
removed './b1/fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc'
removed './b2/fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc'