Running as unit: rb-build-i386_6-56223.service ==================================================================================== Sat Feb 22 15:19:31 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_i386_6) on jenkins, called using "ionos6-i386 ionos12-i386" as arguments. Sat Feb 22 15:19:31 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-eW6Ot3sM" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Feb 22 15:19:31 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos6-i386.debian.net is marked as down. Sat Feb 22 15:19:31 UTC 2025 - checking via ssh if ionos6-i386.debian.net is up. removed '/tmp/read-only-fs-test-YOm4dk' Sat Feb 22 15:19:32 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos12-i386.debian.net is marked as down. Sat Feb 22 15:19:32 UTC 2025 - checking via ssh if ionos12-i386.debian.net is up. removed '/tmp/read-only-fs-test-fbeaNO' ok, let's check if fastqtl is building anywhere yet… ok, fastqtl is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of fastqtl in trixie on i386 on jenkins now. 1st build will be done on ionos6-i386.debian.net. 2nd build will be done on ionos12-i386.debian.net. ============================================================================= 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 1740237574 i386 trixie fastqtl 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] --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 Uploaders: Dylan Aïssi , Étienne Mollier 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 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmV8pfoUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdr1Iw/5ATLST/K+F4rGkq/7N/j5ZxlVLgvh 7alysbz1B+kMipcH8TKc+ira3a+3yb1GuLDxiw+OGolkoWFUdqQ42PiEx2I5Fpyk BOITQ9cZJgw8GVihtRXaqD3sYCmVOlgo0nxfnOFm82zjfOnKYX7riueC1wuiD1iI odpa0cWGPhRKzLycqaZFeF+Unu3QAEGWyj/pGDv//7JHIlc7qK6qZbXi6Y+8Q8vW 7wqwCdB19nkFcQC+wNWuKcyyCKoQ7ZQLJRBloFh8aCGKJ4H+xjSrLKGl964lgK+X LM2EPSuJyAjCiK0V5u7jLYvFvuCOvYBDcHCXwceJO6tMwPJC8+sn1+XXwIx3tUJq 8O+qaBHCE0cjLWTvBzeqx6JMnW7MrrmNYik+9QbSy/3Po9vlU0T5WJLduiswUky7 gBUGFUz39xyYXFkg8eyPoQp0RXB9qVxbtjGxAYPpqjKmLad1UgmQtVYnBTllRGij 4VhfJ2ZzBMH4ciVuFx7ER3tjtIA6NVISGxAveDXDyQqooCHcX++EXeZBVUKbZqQJ AtnI/9S1hJbMDJfDjj4eOUiMWK9ym93Yjp39prkRjtNHQAUdPEulDu6CvLxHb1HM JQFVakiOFFXY6e1jlF32fNFFYBWxOzf6X22/+qwGrzQ+4F4F038+Fz2GObKFIJO8 r6dQ+KWw8G5AuAA= =kyhw -----END PGP SIGNATURE----- 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 15:19:34 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos6-i386.debian.net is marked as down. Sat Feb 22 15:19:34 UTC 2025 - checking via ssh if ionos6-i386.debian.net is up. removed '/tmp/read-only-fs-test-iPFrfK' ==================================================================================== Fri Mar 27 21:42:35 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos6-i386, called using "1 fastqtl trixie /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA 2.184+v7+dfsg-4" as arguments. Fri Mar 27 21:42:36 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-aalXJSxs" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Mar 27 21:42:36 UTC 2026 I: Downloading source for trixie/fastqtl=2.184+v7+dfsg-4 Reading package lists... NOTICE: 'fastqtl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/fastqtl.git Please use: git clone https://salsa.debian.org/med-team/fastqtl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 17.2 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (dsc) [2406 B] Get:2 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (tar) [17.1 MB] Get:3 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (diff) [20.9 kB] Fetched 17.2 MB in 0s (64.6 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'fastqtl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/fastqtl.git Please use: git clone https://salsa.debian.org/med-team/fastqtl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 17.2 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (dsc) [2406 B] Get:2 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (tar) [17.1 MB] Get:3 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (diff) [20.9 kB] Fetched 17.2 MB in 0s (64.6 MB/s) Download complete and in download only mode ============================================================================= Building fastqtl in trixie on i386 on ionos6-i386 now. Date: Fri Mar 27 22:42:37 CET 2026 Date UTC: Fri Mar 27 21:42:37 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log 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 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 ... Selecting previously unselected package libpython3.13-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19844 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_i386.deb ... Unpacking libpython3.13-minimal:i386 (3.13.2-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_i386.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:i386 (3.13.2-1) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20178 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_i386.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:i386. Preparing to unpack .../4-libffi8_3.4.7-1_i386.deb ... Unpacking libffi8:i386 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../6-libreadline8t64_8.2-6_i386.deb ... 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. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_i386.deb ... Unpacking libpython3.13-stdlib:i386 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_i386.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_i386.deb ... Unpacking libpython3-stdlib:i386 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21188 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_i386.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../003-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.23.1-1_i386.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../006-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. 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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.1-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libunbound8:i386 (1.22.0-1+b1) ... Setting up libpkgconf3:i386 (1.8.1-4) ... Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-3) ... Setting up libboost-program-options-dev:i386 (1.83.0.2+b2) ... Setting up comerr-dev:i386 (2.1-1.47.2-1) ... Setting up libunistring5:i386 (1.3-1) ... Setting up libssl-dev:i386 (3.4.1-1) ... Setting up autopoint (0.23.1-1) ... Setting up icu-devtools (72.1-6) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:i386 (1.21.3-4) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8+b1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:i386 (1.6.0-2) ... Setting up libnghttp3-dev:i386 (1.6.0-2) ... Setting up liblzma-dev:i386 (5.6.3-1+b1) ... 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Building tag database... -> 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 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 >&)': src/utils/utils.cpp:133:31: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' 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)': src/analysisPermutation.cpp:75:27: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' 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&, std::vector&)': 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&, std::vector&)': 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 >]' 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 >]' 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&, std::vector&)': 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&, std::vector&)': 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&, std::vector&)': 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&, std::vector&)': 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&, std::vector&)': 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&, std::vector&)': 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 Fri Mar 27 21:43:58 UTC 2026 I: Signing ./b1/fastqtl_2.184+v7+dfsg-4_i386.buildinfo as fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc Fri Mar 27 21:43:59 UTC 2026 I: Signed ./b1/fastqtl_2.184+v7+dfsg-4_i386.buildinfo as ./b1/fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc Fri Mar 27 21:43:59 UTC 2026 - build #1 for fastqtl/trixie/i386 on ionos6-i386 done. Starting cleanup. All cleanup done. Fri Mar 27 21:43:59 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-aalXJSxs, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 15:21 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 15:19 b2 -rw-r--r-- 1 jenkins jenkins 2406 Dec 15 2023 fastqtl_2.184+v7+dfsg-4.dsc -rw------- 1 jenkins jenkins 3541 Feb 22 15:19 rbuildlog.tBvlVUW /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/b1: total 22208 -rw-r--r-- 1 jenkins jenkins 76068 Feb 22 15:21 build.log -rw-r--r-- 1 jenkins jenkins 5254704 Feb 22 15:21 fastqtl-dbgsym_2.184+v7+dfsg-4_i386.deb -rw-r--r-- 1 jenkins jenkins 17104880 Feb 22 15:21 fastqtl-doc_2.184+v7+dfsg-4_all.deb -rw-r--r-- 1 jenkins jenkins 20936 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2406 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4.dsc -rw-r--r-- 1 jenkins jenkins 8705 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 9587 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1954 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4_i386.changes -rw-r--r-- 1 jenkins jenkins 240120 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4_i386.deb -rw-r--r-- 1 jenkins jenkins 1421 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/b2: total 0 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 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 ... Selecting previously unselected package libpython3.13-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19844 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_i386.deb ... Unpacking libpython3.13-minimal:i386 (3.13.2-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_i386.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:i386 (3.13.2-1) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20178 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_i386.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libffi8:i386. Preparing to unpack .../4-libffi8_3.4.7-1_i386.deb ... Unpacking libffi8:i386 (3.4.7-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../6-libreadline8t64_8.2-6_i386.deb ... 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. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_i386.deb ... Unpacking libpython3.13-stdlib:i386 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_i386.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../9-libpython3-stdlib_3.13.1-2_i386.deb ... Unpacking libpython3-stdlib:i386 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21188 files and directories currently installed.) 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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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.1-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libunbound8:i386 (1.22.0-1+b1) ... Setting up libpkgconf3:i386 (1.8.1-4) ... Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-3) ... Setting up libboost-program-options-dev:i386 (1.83.0.2+b2) ... Setting up comerr-dev:i386 (2.1-1.47.2-1) ... Setting up libunistring5:i386 (1.3-1) ... Setting up libssl-dev:i386 (3.4.1-1) ... Setting up autopoint (0.23.1-1) ... Setting up icu-devtools (72.1-6) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:i386 (1.21.3-4) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8+b1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:i386 (1.6.0-2) ... Setting up libnghttp3-dev:i386 (1.6.0-2) ... Setting up liblzma-dev:i386 (5.6.3-1+b1) ... 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Setting up python3-jaraco.text (4.0.0-1) ... Setting up librtmp-dev:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:i386 (1.21.3-4) ... Setting up libhts3t64:i386 (1.21+ds-1) ... Setting up krb5-multidev:i386 (1.21.3-4) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up libkrb5-dev:i386 (1.21.3-4) ... Setting up dh-python (6.20250108) ... Setting up libcurl4-gnutls-dev:i386 (8.12.1-2) ... Setting up libhts-dev:i386 (1.21+ds-1) ... Processing triggers for libc-bin (2.40-7) ... 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/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 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 >&)': src/utils/utils.cpp:133:31: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' 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)': src/analysisPermutation.cpp:75:27: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' 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&, std::vector&)': 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&, std::vector&)': 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 >]' 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 >]' 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&, std::vector&)': 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&, std::vector&)': 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&, std::vector&)': 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&, std::vector&)': 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&, std::vector&)': 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&, std::vector&)': 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 15:21:01 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos12-i386.debian.net is marked as down. Sat Feb 22 15:21:01 UTC 2025 - checking via ssh if ionos12-i386.debian.net is up. removed '/tmp/read-only-fs-test-Cyl24t' ==================================================================================== Sat Feb 22 15:21:02 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos12-i386, called using "2 fastqtl trixie /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA 2.184+v7+dfsg-4" as arguments. Sat Feb 22 15:21:02 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-RjfIiFKZ" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Feb 22 15:21:02 UTC 2025 I: Downloading source for trixie/fastqtl=2.184+v7+dfsg-4 Reading package lists... NOTICE: 'fastqtl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/fastqtl.git Please use: git clone https://salsa.debian.org/med-team/fastqtl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 17.2 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (dsc) [2406 B] Get:2 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (tar) [17.1 MB] Get:3 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (diff) [20.9 kB] Fetched 17.2 MB in 0s (55.5 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'fastqtl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/fastqtl.git Please use: git clone https://salsa.debian.org/med-team/fastqtl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 17.2 MB of source archives. Get:1 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (dsc) [2406 B] Get:2 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (tar) [17.1 MB] Get:3 http://deb.debian.org/debian trixie/main fastqtl 2.184+v7+dfsg-4 (diff) [20.9 kB] Fetched 17.2 MB in 0s (55.5 MB/s) Download complete and in download only mode ============================================================================= Re-Building fastqtl in trixie on i386 on ionos12-i386 now. Date: Sat Feb 22 16:21:02 CET 2025 Date UTC: Sat Feb 22 15:21:02 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/pbuilderrc_ha8l + case ${ARCH} in + let NUM_CPU-=3 + case $ARCH in + locale=de_CH + language=de + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' fastqtl = debian-installer -o fastqtl = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' fastqtl = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/pbuilderrc_ha8l --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/b2 --logfile b2/build.log fastqtl_2.184+v7+dfsg-4.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Feb 23 05:21:03 +14 2025 I: pbuilder-time-stamp: 1740237663 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/27202/tmp/hooks/D01_modify_environment starting debug: Running on ionos12-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Feb 22 15:21 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/27202/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/27202/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=1ab44ec7665e47299eea838e28228180 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=27202 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/pbuilderrc_ha8l --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/b2 --logfile b2/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-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 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 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/27202/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 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 ... 19794 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 (69.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19794 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_i386.deb ... Unpacking libpython3.13-minimal:i386 (3.13.2-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_i386.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:i386 (3.13.2-1) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20128 files and directories currently installed.) 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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. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_i386.deb ... Unpacking libpython3.13-stdlib:i386 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_i386.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:i386. 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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.1-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libunbound8:i386 (1.22.0-1+b1) ... Setting up libpkgconf3:i386 (1.8.1-4) ... Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-3) ... Setting up libboost-program-options-dev:i386 (1.83.0.2+b2) ... Setting up comerr-dev:i386 (2.1-1.47.2-1) ... Setting up libunistring5:i386 (1.3-1) ... Setting up libssl-dev:i386 (3.4.1-1) ... Setting up autopoint (0.23.1-1) ... Setting up icu-devtools (72.1-6) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:i386 (1.21.3-4) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8+b1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:i386 (1.6.0-2) ... Setting up libnghttp3-dev:i386 (1.6.0-2) ... Setting up liblzma-dev:i386 (5.6.3-1+b1) ... 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Setting up libblas-dev:i386 (3.12.1-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up libbz2-dev:i386 (1.0.8-6) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libgmp-dev:i386 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:i386 (3.10-1+b1) ... Setting up libtool (2.5.4-3) ... Setting up libidn2-0:i386 (2.3.7-2+b1) ... Setting up libngtcp2-dev:i386 (1.9.1-1) ... Setting up pkgconf:i386 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:i386 (2.6.9+dfsg-1) ... Setting up libp11-kit0:i386 (0.25.5-3) ... Setting up libeigen3-dev (3.4.0-4) ... 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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) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libngtcp2-crypto-gnutls8:i386 (1.9.1-1) ... Setting up libkadm5clnt-mit12:i386 (1.21.3-4) ... Setting up libgnutls28-dev:i386 (3.8.9-2) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... 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) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:i386 (1.9.1-1) ... 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) ... Setting up libkadm5srv-mit12:i386 (1.21.3-4) ... Setting up libhts3t64:i386 (1.21+ds-1) ... Setting up krb5-multidev:i386 (1.21.3-4) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up libkrb5-dev:i386 (1.21.3-4) ... Setting up dh-python (6.20250108) ... Setting up libcurl4-gnutls-dev:i386 (8.12.1-2) ... Setting up libhts-dev:i386 (1.21+ds-1) ... Processing triggers for libc-bin (2.40-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/27202/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/27202/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/fastqtl-2.184+v7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --with python3 dh_auto_clean make -j10 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 -j10 "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 src/analysisPermutation.cpp: In member function 'void data::runPermutation(std::string, std::vector)': src/analysisPermutation.cpp:75:27: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' 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&, std::vector&)': 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&, std::vector&)': 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 >]' 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 >]' 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/analysisNominal.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': 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/analysisPermutationPerGroup.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': 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&, std::vector&)': 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&, std::vector&)': 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&, std::vector&)': 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 -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 In file included from src/management.cpp:20: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': 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 -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 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"); | ^~~~~~~~~~~~ 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/utils.cpp: In function 'void putils::random_shuffle(std::vector >&)': src/utils/utils.cpp:133:31: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' 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) | ^~~~~~~~~~~~~~ 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/sort_index_pairs.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/merge_chunks.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/run_chunk.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' in '../fastqtl_2.184+v7+dfsg-4_i386.deb'. 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-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: user script /srv/workspace/pbuilder/27202/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/27202/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/27202 and its subdirectories I: Current time: Sun Feb 23 05:23:13 +14 2025 I: pbuilder-time-stamp: 1740237793 + false + set +x Sat Feb 22 15:23:13 UTC 2025 I: Signing ./b2/fastqtl_2.184+v7+dfsg-4_i386.buildinfo as fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc Sat Feb 22 15:23:13 UTC 2025 I: Signed ./b2/fastqtl_2.184+v7+dfsg-4_i386.buildinfo as ./b2/fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc Sat Feb 22 15:23:13 UTC 2025 - build #2 for fastqtl/trixie/i386 on ionos12-i386 done. Starting cleanup. All cleanup done. Sat Feb 22 15:23:13 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-RjfIiFKZ, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA: total 96 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 15:21 b1 drwxr-xr-x 2 jenkins jenkins 4096 Feb 22 15:23 b2 -rw-r--r-- 1 jenkins jenkins 2406 Dec 15 2023 fastqtl_2.184+v7+dfsg-4.dsc -rw------- 1 jenkins jenkins 79894 Feb 22 15:21 rbuildlog.tBvlVUW /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/b1: total 22252 -rw-r--r-- 1 jenkins jenkins 76068 Feb 22 15:21 build.log -rw-r--r-- 1 jenkins jenkins 5254704 Feb 22 15:21 fastqtl-dbgsym_2.184+v7+dfsg-4_i386.deb -rw-r--r-- 1 jenkins jenkins 17104880 Feb 22 15:21 fastqtl-doc_2.184+v7+dfsg-4_all.deb -rw-r--r-- 1 jenkins jenkins 20936 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2406 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4.dsc -rw-r--r-- 1 jenkins jenkins 8705 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 9587 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1954 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4_i386.changes -rw-r--r-- 1 jenkins jenkins 240120 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4_i386.deb -rw-r--r-- 1 jenkins jenkins 1421 Feb 22 15:21 fastqtl_2.184+v7+dfsg-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/b2: total 22212 -rw-r--r-- 1 jenkins jenkins 77971 Feb 22 15:23 build.log -rw-r--r-- 1 jenkins jenkins 5254704 Feb 22 15:23 fastqtl-dbgsym_2.184+v7+dfsg-4_i386.deb -rw-r--r-- 1 jenkins jenkins 17104880 Feb 22 15:23 fastqtl-doc_2.184+v7+dfsg-4_all.deb -rw-r--r-- 1 jenkins jenkins 20936 Feb 22 15:23 fastqtl_2.184+v7+dfsg-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2406 Feb 22 15:23 fastqtl_2.184+v7+dfsg-4.dsc -rw-r--r-- 1 jenkins jenkins 8705 Feb 22 15:23 fastqtl_2.184+v7+dfsg-4_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 9587 Feb 22 15:23 fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1954 Feb 22 15:23 fastqtl_2.184+v7+dfsg-4_i386.changes -rw-r--r-- 1 jenkins jenkins 240120 Feb 22 15:23 fastqtl_2.184+v7+dfsg-4_i386.deb -rw-r--r-- 1 jenkins jenkins 1421 Feb 22 15:23 fastqtl_2.184+v7+dfsg-4_source.changes 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 Changed-By: Étienne Mollier 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 removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/fastqtl_2.184+v7+dfsg-4.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/fastqtl_2.184+v7+dfsg-4.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/fastqtl_2.184+v7+dfsg-4.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/fastqtl_2.184+v7+dfsg-4.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/i386/fastqtl_2.184+v7+dfsg-4_i386.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/fastqtl_2.184+v7+dfsg-4.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-02-22 15:21:00.299061755 +0000 +++ b2/build.log 2025-02-22 15:23:14.156982808 +0000 @@ -1,6 +1,6 @@ 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: Current time: Sun Feb 23 05:21:03 +14 2025 +I: pbuilder-time-stamp: 1740237663 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,54 +29,86 @@ 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: user script /srv/workspace/pbuilder/27202/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 22 15:21 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/27202/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27202/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + 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='> ' + INVOCATION_ID=1ab44ec7665e47299eea838e28228180 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=27202 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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/pbuilderrc_ha8l --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/b2 --logfile b2/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-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 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 + Linux i-capture-the-hostname 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 + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/27202/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -89,7 +121,7 @@ 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.) +(Reading database ... 19794 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: @@ -274,10 +306,10 @@ 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) +Fetched 78.1 MB in 1s (69.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:i386. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19844 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19794 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.2-1_i386.deb ... Unpacking libpython3.13-minimal:i386 (3.13.2-1) ... Selecting previously unselected package libexpat1:i386. @@ -290,7 +322,7 @@ Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20178 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20128 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.1-2_i386.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. @@ -326,7 +358,7 @@ Unpacking libpython3-stdlib:i386 (3.13.1-2) ... Setting up python3-minimal (3.13.1-2) ... Selecting previously unselected package python3. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21188 files and directories currently installed.) +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21138 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.1-2_i386.deb ... Unpacking python3 (3.13.1-2) ... Selecting previously unselected package sensible-utils. @@ -731,8 +763,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Mar 27 21:43:06 UTC 2026. -Universal Time is now: Fri Mar 27 21:43:06 UTC 2026. +Local time is now: Sat Feb 22 15:21:41 UTC 2025. +Universal Time is now: Sat Feb 22 15:21:41 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -855,7 +887,11 @@ Building tag database... -> 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 +I: user script /srv/workspace/pbuilder/27202/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/27202/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/fastqtl-2.184+v7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 @@ -865,7 +901,7 @@ debian/rules clean dh clean --with python3 dh_auto_clean - make -j22 clean + make -j10 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' @@ -880,7 +916,7 @@ 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 -j10 "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 @@ -892,37 +928,6 @@ 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 >&)': -src/utils/utils.cpp:133:31: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' 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)': src/analysisPermutation.cpp:75:27: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 75 | random_shuffle(phenotype_curr.begin(), phenotype_curr.end()); @@ -945,7 +950,7 @@ 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: +In file included from src/analysisNominalBest.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -974,7 +979,7 @@ /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: +In file included from src/analysisNominal.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -986,7 +991,7 @@ 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: +In file included from src/analysisPermutationPerGroup.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -998,7 +1003,7 @@ 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: +In file included from src/analysisPermutationSequence.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -1021,7 +1026,7 @@ 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: +In file included from src/analysisMapping.cpp:17: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -1033,7 +1038,16 @@ 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: +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 +In file included from src/management.cpp:20: src/data.h: In member function 'double data::getCorrelation(std::vector&, std::vector&)': src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 180 | case 3: sum0 += vec1[i+2] * vec2[i+2]; @@ -1045,6 +1059,28 @@ src/data.h:182:9: note: here 182 | case 1: sum0 += vec1[i+0] * vec2[i+0]; | ^~~~ +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 +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"); + | ^~~~~~~~~~~~ +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/utils.cpp: In function 'void putils::random_shuffle(std::vector >&)': +src/utils/utils.cpp:133:31: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' 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) + | ^~~~~~~~~~~~~~ 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/ && \ @@ -1065,11 +1101,11 @@ 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/annotate_outputs.py I: dh_python3 tools:113: replacing shebang in debian/fastqtl/usr/bin/merge_chunks.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/run_chunk.py dh_lintian dh_perl dh_link @@ -1090,9 +1126,9 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'fastqtl' in '../fastqtl_2.184+v7+dfsg-4_i386.deb'. 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) @@ -1100,12 +1136,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/27202/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27202/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/103323 and its subdirectories -I: Current time: Fri Mar 27 09:43:58 -12 2026 -I: pbuilder-time-stamp: 1774647838 +I: removing directory /srv/workspace/pbuilder/27202 and its subdirectories +I: Current time: Sun Feb 23 05:23:13 +14 2025 +I: pbuilder-time-stamp: 1740237793 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/fastqtl_2.184+v7+dfsg-4.diff: 82.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/fastqtl_2.184+v7+dfsg-4.diff.gz b2/build.log: 83.5% -- replaced with stdout Compressing the 1st log... b1/build.log: 84.0% -- replaced with stdout Sat Feb 22 15:23:15 UTC 2025 I: diffoscope 289 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_fastqtl_trixie_i386_1740237795 + touch /var/log/reproducible-builds/diffoscope_stamp_fastqtl_trixie_i386_1740237795 + RESULT=0 + systemd-run '--description=diffoscope on fastqtl/2.184+v7+dfsg-4 in trixie/i386' --slice=rb-build-diffoscope.slice -u rb-diffoscope-i386_6-56223 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA --run-session -c jenkins-reproducible-trixie-diffoscope-29f1d669-5f99-4b8f-a810-92472cecd69f -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.Y6S2OnGA/dbd-tmp-o7UFtIf ; timeout 150m 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' + false + set +x 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. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-02-22 15:23:16] INFO: Starting at 2025-02-22 15:23:16.923631 [2025-02-22 15:23:16] INFO: Generating the pages of 1 package(s) [2025-02-22 15:23:17] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/i386/fastqtl didn't produce a buildlog, even though it has been built. [2025-02-22 15:23:17] INFO: Finished at 2025-02-22 15:23:17.536646, took: 0:00:00.613023 Sat Feb 22 15:23:17 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/i386/fastqtl.html 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 https://buildinfo.debian.net/f6f258dfc6991aa74d89c155dc207d1ff84608ad/fastqtl_2.184+v7+dfsg-4_all Sat Feb 22 15:23:19 UTC 2025 I: Submitting 12K b2/fastqtl_2.184+v7+dfsg-4_i386.buildinfo.asc https://buildinfo.debian.net/cca856e5f6c2b2b457bad38bb27903d41ef6d462/fastqtl_2.184+v7+dfsg-4_all 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' 1740237800 i386 trixie fastqtl Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/fastqtl_2.184+v7+dfsg-4.rbuild.log: 81.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/fastqtl_2.184+v7+dfsg-4.rbuild.log.gz [2025-02-22 15:23:21] INFO: Starting at 2025-02-22 15:23:21.226622 [2025-02-22 15:23:21] INFO: Generating the pages of 1 package(s) [2025-02-22 15:23:21] INFO: Finished at 2025-02-22 15:23:21.792633, took: 0:00:00.566018 All cleanup done. Sat Feb 22 15:23:21 UTC 2025 - total duration: 0h 3m 45s. Sat Feb 22 15:23:21 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-eW6Ot3sM, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 3min 50.190s CPU time consumed: 7.562s