Running as unit: rb-build-arm64_5-69481.service ==================================================================================== Thu Nov 21 15:29:47 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_5) on jenkins, called using "codethink03-arm64 codethink01-arm64" as arguments. Thu Nov 21 15:29:47 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-gACYQRM9" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 15:29:47 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Thu Nov 21 15:29:47 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-wRpfk6' Thu Nov 21 15:29:48 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Thu Nov 21 15:29:48 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-cq7EUC' ok, let's check if daligner is building anywhere yet… ok, daligner is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of daligner in trixie on arm64 on jenkins now. 1st build will be done on codethink03-arm64.debian.net. 2nd build will be done on codethink01-arm64.debian.net. ============================================================================= Thu Nov 21 15:29:51 UTC 2024 I: starting to build daligner/trixie/arm64 on jenkins on '2024-11-21 15:29' Thu Nov 21 15:29:51 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_5/69481/console.log 1732202991 arm64 trixie daligner Thu Nov 21 15:29:51 UTC 2024 I: Downloading source for trixie/daligner=1.0+git20240119.335105d-3 --2024-11-21 15:29:52-- http://deb.debian.org/debian/pool/main/d/daligner/daligner_1.0%2bgit20240119.335105d-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2287 (2.2K) [text/prs.lines.tag] Saving to: ‘daligner_1.0+git20240119.335105d-3.dsc’ 0K .. 100% 364M=0s 2024-11-21 15:29:52 (364 MB/s) - ‘daligner_1.0+git20240119.335105d-3.dsc’ saved [2287/2287] --2024-11-21 15:29:52-- http://deb.debian.org/debian/pool/main/d/daligner/daligner_1.0%2bgit20240119.335105d-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2287 (2.2K) [text/prs.lines.tag] Saving to: ‘daligner_1.0+git20240119.335105d-3.dsc’ 0K .. 100% 364M=0s 2024-11-21 15:29:52 (364 MB/s) - ‘daligner_1.0+git20240119.335105d-3.dsc’ saved [2287/2287] Thu Nov 21 15:29:52 UTC 2024 I: daligner_1.0+git20240119.335105d-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: daligner Binary: daligner Architecture: any Version: 1.0+git20240119.335105d-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://dazzlerblog.wordpress.com Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/daligner Vcs-Git: https://salsa.debian.org/med-team/daligner.git Testsuite: autopkgtest Testsuite-Triggers: dazzdb Build-Depends: debhelper-compat (= 13) Package-List: daligner deb science optional arch=any Checksums-Sha1: c8c497f24b3b4df81b92b7c32558949c7196a298 128472 daligner_1.0+git20240119.335105d.orig.tar.xz d83b87746857e14a5d7f1cd5527b5467b4324fa2 6660 daligner_1.0+git20240119.335105d-3.debian.tar.xz Checksums-Sha256: a222e15f650e878dbb3395a95b896a88b83f529830e858945549f17c286622b9 128472 daligner_1.0+git20240119.335105d.orig.tar.xz a8354ecc485718a48fe0448a6f70f393fc191d082d6c59eabfa781443f63dc6f 6660 daligner_1.0+git20240119.335105d-3.debian.tar.xz Files: 0d7b712d302f1308d3f021e247c49065 128472 daligner_1.0+git20240119.335105d.orig.tar.xz 4ceab3dd0c1fe15c0124ebbcaead4e0e 6660 daligner_1.0+git20240119.335105d-3.debian.tar.xz Dgit: e54816c7eec1edc38760e9b623bcf67634916e8b debian archive/debian/1.0+git20240119.335105d-3 https://git.dgit.debian.org/daligner -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmaFuRAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdoCUg/6AjvsSjuzwVyOW89h3h7t49lMecBK 2sf+bdo1XnHc8eldjImat3TNWP7E1j19S/SDq5e9SyDGv1qkshb7uvfAuFlA6YRd nlydxTfla0bRE37jo7iKYhpMk6G/6qyumIcV+/r5ZBotzdDDVF7D9ddYEnX4vZWf tQkxdmdNjUVKcFKgEJl+j0bVRPQdXlefqOO4HxXcSqHeCXxo7aSnxdCnQzp+P6LU SecXX/sp85u861ib1/28+U4cvyGqKN5p2/7e2nETwfXgJPbBpVxYG3AMqPNn1hwa ZjAFHegsQZdAdaXfyMwcm2QrJvRwWeFzrWX6rBNHsvUQPGIhA01RJ6YBkQfHHbsF hzV6SZvcM6Sr6Vm7/11FhwHQmnWiSae7lKFSYssOsrMUZJNtf4cAfr0kE3vdHK2Q 29tyF1xa7zZ0RSMWC3UXZ0q80wDok/aL8d9gXDCVyWWJwIDg21f8ttFqWkynxK6k zQgyqx1su3uhXpzo+IGCy+bY1w6zQLH9gGMyoD0INx+y0hI38TlC3xJZ9RAGlNYu bmCcMcikj20H+vdXVl+N9SejJ+eAthA/5jPto4hsGac0VE5WHVleNK2PlXKe59hP 7vg5wBDPJVHh2VhYAAu0tbh566WafdYcWaJfgjez1NmQMLkL+hyNEfQvFABbqCQS QKFSpF3VZeaLxFc= =saI+ -----END PGP SIGNATURE----- Thu Nov 21 15:29:52 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 15:29:52 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Thu Nov 21 15:29:52 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Thu Nov 21 15:29:52 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Thu Nov 21 15:29:52 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-rURcTp' ==================================================================================== Wed Dec 24 21:52:53 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "1 daligner trixie /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z 1.0+git20240119.335105d-3" as arguments. Wed Dec 24 21:52:53 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-NrtZtjsH" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Dec 24 21:52:53 UTC 2025 I: Downloading source for trixie/daligner=1.0+git20240119.335105d-3 Reading package lists... NOTICE: 'daligner' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/daligner.git Please use: git clone https://salsa.debian.org/med-team/daligner.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 137 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (dsc) [2287 B] Get:2 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (tar) [128 kB] Get:3 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (diff) [6660 B] Fetched 137 kB in 0s (5510 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'daligner' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/daligner.git Please use: git clone https://salsa.debian.org/med-team/daligner.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 137 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (dsc) [2287 B] Get:2 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (tar) [128 kB] Get:3 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (diff) [6660 B] Fetched 137 kB in 0s (5510 kB/s) Download complete and in download only mode ============================================================================= Building daligner in trixie on arm64 on codethink03-arm64 now. Date: Wed Dec 24 21:52:53 GMT 2025 Date UTC: Wed Dec 24 21:52:53 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 24 09:52:54 -12 2025 I: pbuilder-time-stamp: 1766613174 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [daligner_1.0+git20240119.335105d-3.dsc] I: copying [./daligner_1.0+git20240119.335105d.orig.tar.xz] I: copying [./daligner_1.0+git20240119.335105d-3.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Jul 3 20:48:16 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./daligner_1.0+git20240119.335105d-3.dsc: no acceptable signature found dpkg-source: info: extracting daligner in daligner-1.0+git20240119.335105d dpkg-source: info: unpacking daligner_1.0+git20240119.335105d.orig.tar.xz dpkg-source: info: unpacking daligner_1.0+git20240119.335105d-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cflags.patch dpkg-source: info: applying lddflags.patch dpkg-source: info: applying destdir-install.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying cppflags.patch dpkg-source: info: applying fix-missing-include.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2314927/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='0481c53b68cb4bff9c484c70d12b4fd7' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2314927' 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.XzNRJF8z/pbuilderrc_NE9P --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.XzNRJF8z/b1 --logfile b1/build.log daligner_1.0+git20240119.335105d-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2314927/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20087 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. 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 77.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Fetched 19.4 MB in 0s (123 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/daligner-1.0+git20240119.335105d/ && 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 > ../daligner_1.0+git20240119.335105d-3_source.changes dpkg-buildpackage: info: source package daligner dpkg-buildpackage: info: source version 1.0+git20240119.335105d-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' rm -f daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LA2ONE LAcheck ONE2LA rm -fr *.dSYM rm -f daligner.tar.gz make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o HPC.daligner HPC.daligner.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAsort LAsort.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAmerge LAmerge.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAsplit LAsplit.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAcat LAcat.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAshow LAshow.c align.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAcheck LAcheck.c align.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm -Wl,-z,relro -Wl,-z,now LAshow.c: In function 'main': LAshow.c:415:36: warning: variable 'lhalf' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~~ LAshow.c:415:30: warning: variable 'seen' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~ LAshow.c:415:23: warning: variable 'match' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~~ LAshow.c:415:16: warning: variable 'blast' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~~ ONE2LA.c: In function 'main': ONE2LA.c:30:20: warning: variable 'small' set but not used [-Wunused-but-set-variable] 30 | int tspace, small, tbytes; | ^~~~~ LAshow.c:743:5: warning: 'bmap' may be used uninitialized [-Wmaybe-uninitialized] 743 | free(bmap); | ^~~~~~~~~~ LAshow.c:55:11: note: 'bmap' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~ LAshow.c:549:25: warning: 'blen' may be used uninitialized [-Wmaybe-uninitialized] 549 | blens = blen[bread]; | ^ LAshow.c:55:18: note: 'blen' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~ LAshow.c:588:40: warning: 'bctg' may be used uninitialized [-Wmaybe-uninitialized] 588 | printf(".%0*d",bc_wide,bctg[bread]+1); | ^ LAshow.c:55:25: note: 'bctg' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~ LAshow.c:448:19: warning: 'nbscaff' may be used uninitialized [-Wmaybe-uninitialized] 448 | { br_wide = Number_Digits((int64) nbscaff); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:55:31: note: 'nbscaff' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~~~~ LAshow.c:449:19: warning: 'bmaxlen' may be used uninitialized [-Wmaybe-uninitialized] 449 | bi_wide = Number_Digits((int64) bmaxlen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:55:40: note: 'bmaxlen' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~~~~ LAshow.c:450:19: warning: 'bctgmax' may be used uninitialized [-Wmaybe-uninitialized] 450 | bc_wide = Number_Digits((int64) bctgmax); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:55:49: note: 'bctgmax' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~~~~ LAshow.c:744:3: warning: 'amap' may be used uninitialized [-Wmaybe-uninitialized] 744 | free(amap); | ^~~~~~~~~~ LAshow.c:54:11: note: 'amap' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~ LAshow.c:541:25: warning: 'alen' may be used uninitialized [-Wmaybe-uninitialized] 541 | alens = alen[aread]; | ^ LAshow.c:54:18: note: 'alen' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~ LAshow.c:581:40: warning: 'actg' may be used uninitialized [-Wmaybe-uninitialized] 581 | printf(".%0*d",ac_wide,actg[aread]+1); | ^ LAshow.c:54:25: note: 'actg' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~ LAshow.c:439:19: warning: 'nascaff' may be used uninitialized [-Wmaybe-uninitialized] 439 | { ar_wide = Number_Digits((int64) nascaff); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:54:31: note: 'nascaff' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~~~~ LAshow.c:440:19: warning: 'amaxlen' may be used uninitialized [-Wmaybe-uninitialized] 440 | ai_wide = Number_Digits((int64) amaxlen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:54:40: note: 'amaxlen' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~~~~ LAshow.c:441:19: warning: 'actgmax' may be used uninitialized [-Wmaybe-uninitialized] 441 | ac_wide = Number_Digits((int64) actgmax); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:54:49: note: 'actgmax' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~~~~ filter.c: In function 'report_thread': filter.c:2155:23: warning: suggest braces around empty body in an 'else' statement [-Wempty-body] 2155 | ; | ^ ONElib.c: In function 'oneSchemaCreateDynamic': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:392:3: note: in expansion of macro 'assert' 392 | assert (fileType && strlen(fileType) > 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:393:3: note: in expansion of macro 'assert' 393 | assert (!subType || strlen(subType) > 0) ; | ^~~~~~ ONElib.c: In function 'readBuf': ONElib.c:616:40: warning: comparison is always false due to limited range of data type [-Wtype-limits] 616 | if (isspace(x) || x == '\0' || x == EOF) | ^~ ONElib.c: In function 'readString': ONElib.c:664:32: warning: comparison is always false due to limited range of data type [-Wtype-limits] 664 | if (*cp == '\n' || *cp == EOF) | ^~ ONElib.c: In function 'readFlush': ONElib.c:695:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 695 | if (x == EOF) | ^~ ONElib.c: In function 'oneReadLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:945:3: note: in expansion of macro 'assert' 945 | assert (!vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:946:3: note: in expansion of macro 'assert' 946 | assert (!vf->isFinal) ; | ^~~~~~ ONElib.c: In function 'oneFileOpenRead': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1158:3: note: in expansion of macro 'assert' 1158 | assert (fileType == NULL || strlen(fileType) > 0) ; | ^~~~~~ ONElib.c: In function 'addProvenance': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1760:3: note: in expansion of macro 'assert' 1760 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'addReference': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1811:3: note: in expansion of macro 'assert' 1811 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'writeHeader': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1885:3: note: in expansion of macro 'assert' 1885 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1886:3: note: in expansion of macro 'assert' 1886 | assert (vf->line == 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1887:3: note: in expansion of macro 'assert' 1887 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'oneWriteLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2029:3: note: in expansion of macro 'assert' 2029 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2030:3: note: in expansion of macro 'assert' 2030 | assert (!vf->isFinal || !isalpha(t)) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2033:3: note: in expansion of macro 'assert' 2033 | assert (li) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2040:7: note: in expansion of macro 'assert' 2040 | { assert (listLen >= 0) ; | ^~~~~~ ONElib.c: In function 'oneFileClose': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2488:3: note: in expansion of macro 'assert' 2488 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'intGet': ONElib.c:3490:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3490 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3491:9: note: here 3491 | case 1: *pval = *(I64*)(u+1) & 0x0000000000ffff ; return 3 ; | ^~~~ ONElib.c:3502:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3502 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3503:9: note: here 3503 | case 1: *pval = *(I64*)(u+1) | 0xffffffffffff0000 ; return 3 ; | ^~~~ ONElib.c:3488:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 3488 | switch (u[0] & 0x07) | ^~~~~~ ONElib.c:3499:5: note: here 3499 | case 4: | ^~~~ ONElib.c: In function 'ltfRead': ONElib.c:3564:10: warning: 'val' may be used uninitialized [-Wmaybe-uninitialized] 3564 | return val ; | ^~~ ONElib.c:3544:7: note: 'val' was declared here 3544 | I64 val ; | ^~~ ONElib.c: In function 'oneSchemaCreateDynamic': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:392:3: note: in expansion of macro 'assert' 392 | assert (fileType && strlen(fileType) > 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:393:3: note: in expansion of macro 'assert' 393 | assert (!subType || strlen(subType) > 0) ; | ^~~~~~ ONElib.c: In function 'readBuf': ONElib.c:616:40: warning: comparison is always false due to limited range of data type [-Wtype-limits] 616 | if (isspace(x) || x == '\0' || x == EOF) | ^~ ONElib.c: In function 'readString': ONElib.c:664:32: warning: comparison is always false due to limited range of data type [-Wtype-limits] 664 | if (*cp == '\n' || *cp == EOF) | ^~ ONElib.c: In function 'readFlush': ONElib.c:695:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 695 | if (x == EOF) | ^~ ONElib.c: In function 'oneReadLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:945:3: note: in expansion of macro 'assert' 945 | assert (!vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:946:3: note: in expansion of macro 'assert' 946 | assert (!vf->isFinal) ; | ^~~~~~ ONElib.c: In function 'oneFileOpenRead': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1158:3: note: in expansion of macro 'assert' 1158 | assert (fileType == NULL || strlen(fileType) > 0) ; | ^~~~~~ ONElib.c: In function 'addProvenance': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1760:3: note: in expansion of macro 'assert' 1760 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'addReference': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1811:3: note: in expansion of macro 'assert' 1811 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'writeHeader': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1885:3: note: in expansion of macro 'assert' 1885 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1886:3: note: in expansion of macro 'assert' 1886 | assert (vf->line == 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1887:3: note: in expansion of macro 'assert' 1887 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'oneWriteLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2029:3: note: in expansion of macro 'assert' 2029 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2030:3: note: in expansion of macro 'assert' 2030 | assert (!vf->isFinal || !isalpha(t)) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2033:3: note: in expansion of macro 'assert' 2033 | assert (li) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2040:7: note: in expansion of macro 'assert' 2040 | { assert (listLen >= 0) ; | ^~~~~~ ONElib.c: In function 'oneFileClose': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2488:3: note: in expansion of macro 'assert' 2488 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'intGet': ONElib.c:3490:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3490 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3491:9: note: here 3491 | case 1: *pval = *(I64*)(u+1) & 0x0000000000ffff ; return 3 ; | ^~~~ ONElib.c:3502:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3502 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3503:9: note: here 3503 | case 1: *pval = *(I64*)(u+1) | 0xffffffffffff0000 ; return 3 ; | ^~~~ ONElib.c:3488:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 3488 | switch (u[0] & 0x07) | ^~~~~~ ONElib.c:3499:5: note: here 3499 | case 4: | ^~~~ ONElib.c: In function 'ltfRead': ONElib.c:3564:10: warning: 'val' may be used uninitialized [-Wmaybe-uninitialized] 3564 | return val ; | ^~~ ONElib.c:3544:7: note: 'val' was declared here 3544 | I64 val ; | ^~~ ONElib.c: In function 'oneFileOpenWriteFrom': ONElib.c:395:33: warning: '%ld' directive writing between 1 and 19 bytes into a region of size between 7 and 25 [-Wformat-overflow=] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~ In function 'oneSchemaCreateDynamic', inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: ONElib.c:395:20: note: directive argument in the range [0, 9223372036854775805] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ONElib.c:22: In function 'sprintf', inlined from 'oneSchemaCreateDynamic' at ONElib.c:395:5, inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 or more bytes (assuming 47) into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ONElib.c: In function 'oneFileOpenWriteFrom': ONElib.c:395:33: warning: '%ld' directive writing between 1 and 19 bytes into a region of size between 7 and 25 [-Wformat-overflow=] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~ In function 'oneSchemaCreateDynamic', inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: ONElib.c:395:20: note: directive argument in the range [0, 9223372036854775805] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ONElib.c:22: In function 'sprintf', inlined from 'oneSchemaCreateDynamic' at ONElib.c:395:5, inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 or more bytes (assuming 47) into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_auto_install make -j12 install DESTDIR=/build/reproducible-path/daligner-1.0\+git20240119.335105d/debian/daligner AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' install -d /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin install daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LA2ONE LAcheck ONE2LA /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin make[2]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' mkdir -p /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/share/man/man1 for command in /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin/*; \ do \ if [ $(basename $command) != daligner ] ; \ then \ ln -s daligner.1 \ /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/share/man/man1/$(basename $command).1 ; \ fi; \ done make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'daligner' in '../daligner_1.0+git20240119.335105d-3_arm64.deb'. dpkg-deb: building package 'daligner-dbgsym' in '../daligner-dbgsym_1.0+git20240119.335105d-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../daligner_1.0+git20240119.335105d-3_arm64.buildinfo dpkg-genchanges --build=binary -O../daligner_1.0+git20240119.335105d-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2314927 and its subdirectories I: Current time: Wed Dec 24 09:53:31 -12 2025 I: pbuilder-time-stamp: 1766613211 Wed Dec 24 21:53:31 UTC 2025 I: Signing ./b1/daligner_1.0+git20240119.335105d-3_arm64.buildinfo as daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc Wed Dec 24 21:53:31 UTC 2025 I: Signed ./b1/daligner_1.0+git20240119.335105d-3_arm64.buildinfo as ./b1/daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc Wed Dec 24 21:53:31 UTC 2025 - build #1 for daligner/trixie/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Wed Dec 24 21:53:31 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-NrtZtjsH, removing. /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 15:30 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 15:29 b2 -rw-r--r-- 1 jenkins jenkins 2287 Jul 3 20:55 daligner_1.0+git20240119.335105d-3.dsc -rw------- 1 jenkins jenkins 3491 Nov 21 15:29 rbuildlog.dvxg5w6 /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/b1: total 1992 -rw-r--r-- 1 jenkins jenkins 43142 Nov 21 15:30 build.log -rw-r--r-- 1 jenkins jenkins 1743336 Nov 21 15:30 daligner-dbgsym_1.0+git20240119.335105d-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 6660 Nov 21 15:30 daligner_1.0+git20240119.335105d-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2287 Nov 21 15:30 daligner_1.0+git20240119.335105d-3.dsc -rw-r--r-- 1 jenkins jenkins 5094 Nov 21 15:30 daligner_1.0+git20240119.335105d-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5976 Nov 21 15:30 daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1666 Nov 21 15:30 daligner_1.0+git20240119.335105d-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 212472 Nov 21 15:30 daligner_1.0+git20240119.335105d-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 1501 Nov 21 15:30 daligner_1.0+git20240119.335105d-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/b2: total 0 Thu Nov 21 15:30:33 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 24 09:52:54 -12 2025 I: pbuilder-time-stamp: 1766613174 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [daligner_1.0+git20240119.335105d-3.dsc] I: copying [./daligner_1.0+git20240119.335105d.orig.tar.xz] I: copying [./daligner_1.0+git20240119.335105d-3.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Jul 3 20:48:16 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./daligner_1.0+git20240119.335105d-3.dsc: no acceptable signature found dpkg-source: info: extracting daligner in daligner-1.0+git20240119.335105d dpkg-source: info: unpacking daligner_1.0+git20240119.335105d.orig.tar.xz dpkg-source: info: unpacking daligner_1.0+git20240119.335105d-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cflags.patch dpkg-source: info: applying lddflags.patch dpkg-source: info: applying destdir-install.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying cppflags.patch dpkg-source: info: applying fix-missing-include.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2314927/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='0481c53b68cb4bff9c484c70d12b4fd7' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2314927' 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.XzNRJF8z/pbuilderrc_NE9P --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.XzNRJF8z/b1 --logfile b1/build.log daligner_1.0+git20240119.335105d-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2314927/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20087 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. 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 77.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Fetched 19.4 MB in 0s (123 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/daligner-1.0+git20240119.335105d/ && 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 > ../daligner_1.0+git20240119.335105d-3_source.changes dpkg-buildpackage: info: source package daligner dpkg-buildpackage: info: source version 1.0+git20240119.335105d-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' rm -f daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LA2ONE LAcheck ONE2LA rm -fr *.dSYM rm -f daligner.tar.gz make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o HPC.daligner HPC.daligner.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAsort LAsort.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAmerge LAmerge.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAsplit LAsplit.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAcat LAcat.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAshow LAshow.c align.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAcheck LAcheck.c align.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm -Wl,-z,relro -Wl,-z,now LAshow.c: In function 'main': LAshow.c:415:36: warning: variable 'lhalf' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~~ LAshow.c:415:30: warning: variable 'seen' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~ LAshow.c:415:23: warning: variable 'match' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~~ LAshow.c:415:16: warning: variable 'blast' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~~ ONE2LA.c: In function 'main': ONE2LA.c:30:20: warning: variable 'small' set but not used [-Wunused-but-set-variable] 30 | int tspace, small, tbytes; | ^~~~~ LAshow.c:743:5: warning: 'bmap' may be used uninitialized [-Wmaybe-uninitialized] 743 | free(bmap); | ^~~~~~~~~~ LAshow.c:55:11: note: 'bmap' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~ LAshow.c:549:25: warning: 'blen' may be used uninitialized [-Wmaybe-uninitialized] 549 | blens = blen[bread]; | ^ LAshow.c:55:18: note: 'blen' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~ LAshow.c:588:40: warning: 'bctg' may be used uninitialized [-Wmaybe-uninitialized] 588 | printf(".%0*d",bc_wide,bctg[bread]+1); | ^ LAshow.c:55:25: note: 'bctg' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~ LAshow.c:448:19: warning: 'nbscaff' may be used uninitialized [-Wmaybe-uninitialized] 448 | { br_wide = Number_Digits((int64) nbscaff); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:55:31: note: 'nbscaff' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~~~~ LAshow.c:449:19: warning: 'bmaxlen' may be used uninitialized [-Wmaybe-uninitialized] 449 | bi_wide = Number_Digits((int64) bmaxlen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:55:40: note: 'bmaxlen' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~~~~ LAshow.c:450:19: warning: 'bctgmax' may be used uninitialized [-Wmaybe-uninitialized] 450 | bc_wide = Number_Digits((int64) bctgmax); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:55:49: note: 'bctgmax' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~~~~ LAshow.c:744:3: warning: 'amap' may be used uninitialized [-Wmaybe-uninitialized] 744 | free(amap); | ^~~~~~~~~~ LAshow.c:54:11: note: 'amap' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~ LAshow.c:541:25: warning: 'alen' may be used uninitialized [-Wmaybe-uninitialized] 541 | alens = alen[aread]; | ^ LAshow.c:54:18: note: 'alen' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~ LAshow.c:581:40: warning: 'actg' may be used uninitialized [-Wmaybe-uninitialized] 581 | printf(".%0*d",ac_wide,actg[aread]+1); | ^ LAshow.c:54:25: note: 'actg' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~ LAshow.c:439:19: warning: 'nascaff' may be used uninitialized [-Wmaybe-uninitialized] 439 | { ar_wide = Number_Digits((int64) nascaff); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:54:31: note: 'nascaff' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~~~~ LAshow.c:440:19: warning: 'amaxlen' may be used uninitialized [-Wmaybe-uninitialized] 440 | ai_wide = Number_Digits((int64) amaxlen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:54:40: note: 'amaxlen' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~~~~ LAshow.c:441:19: warning: 'actgmax' may be used uninitialized [-Wmaybe-uninitialized] 441 | ac_wide = Number_Digits((int64) actgmax); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:54:49: note: 'actgmax' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~~~~ filter.c: In function 'report_thread': filter.c:2155:23: warning: suggest braces around empty body in an 'else' statement [-Wempty-body] 2155 | ; | ^ ONElib.c: In function 'oneSchemaCreateDynamic': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:392:3: note: in expansion of macro 'assert' 392 | assert (fileType && strlen(fileType) > 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:393:3: note: in expansion of macro 'assert' 393 | assert (!subType || strlen(subType) > 0) ; | ^~~~~~ ONElib.c: In function 'readBuf': ONElib.c:616:40: warning: comparison is always false due to limited range of data type [-Wtype-limits] 616 | if (isspace(x) || x == '\0' || x == EOF) | ^~ ONElib.c: In function 'readString': ONElib.c:664:32: warning: comparison is always false due to limited range of data type [-Wtype-limits] 664 | if (*cp == '\n' || *cp == EOF) | ^~ ONElib.c: In function 'readFlush': ONElib.c:695:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 695 | if (x == EOF) | ^~ ONElib.c: In function 'oneReadLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:945:3: note: in expansion of macro 'assert' 945 | assert (!vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:946:3: note: in expansion of macro 'assert' 946 | assert (!vf->isFinal) ; | ^~~~~~ ONElib.c: In function 'oneFileOpenRead': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1158:3: note: in expansion of macro 'assert' 1158 | assert (fileType == NULL || strlen(fileType) > 0) ; | ^~~~~~ ONElib.c: In function 'addProvenance': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1760:3: note: in expansion of macro 'assert' 1760 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'addReference': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1811:3: note: in expansion of macro 'assert' 1811 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'writeHeader': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1885:3: note: in expansion of macro 'assert' 1885 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1886:3: note: in expansion of macro 'assert' 1886 | assert (vf->line == 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1887:3: note: in expansion of macro 'assert' 1887 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'oneWriteLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2029:3: note: in expansion of macro 'assert' 2029 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2030:3: note: in expansion of macro 'assert' 2030 | assert (!vf->isFinal || !isalpha(t)) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2033:3: note: in expansion of macro 'assert' 2033 | assert (li) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2040:7: note: in expansion of macro 'assert' 2040 | { assert (listLen >= 0) ; | ^~~~~~ ONElib.c: In function 'oneFileClose': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2488:3: note: in expansion of macro 'assert' 2488 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'intGet': ONElib.c:3490:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3490 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3491:9: note: here 3491 | case 1: *pval = *(I64*)(u+1) & 0x0000000000ffff ; return 3 ; | ^~~~ ONElib.c:3502:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3502 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3503:9: note: here 3503 | case 1: *pval = *(I64*)(u+1) | 0xffffffffffff0000 ; return 3 ; | ^~~~ ONElib.c:3488:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 3488 | switch (u[0] & 0x07) | ^~~~~~ ONElib.c:3499:5: note: here 3499 | case 4: | ^~~~ ONElib.c: In function 'ltfRead': ONElib.c:3564:10: warning: 'val' may be used uninitialized [-Wmaybe-uninitialized] 3564 | return val ; | ^~~ ONElib.c:3544:7: note: 'val' was declared here 3544 | I64 val ; | ^~~ ONElib.c: In function 'oneSchemaCreateDynamic': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:392:3: note: in expansion of macro 'assert' 392 | assert (fileType && strlen(fileType) > 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:393:3: note: in expansion of macro 'assert' 393 | assert (!subType || strlen(subType) > 0) ; | ^~~~~~ ONElib.c: In function 'readBuf': ONElib.c:616:40: warning: comparison is always false due to limited range of data type [-Wtype-limits] 616 | if (isspace(x) || x == '\0' || x == EOF) | ^~ ONElib.c: In function 'readString': ONElib.c:664:32: warning: comparison is always false due to limited range of data type [-Wtype-limits] 664 | if (*cp == '\n' || *cp == EOF) | ^~ ONElib.c: In function 'readFlush': ONElib.c:695:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 695 | if (x == EOF) | ^~ ONElib.c: In function 'oneReadLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:945:3: note: in expansion of macro 'assert' 945 | assert (!vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:946:3: note: in expansion of macro 'assert' 946 | assert (!vf->isFinal) ; | ^~~~~~ ONElib.c: In function 'oneFileOpenRead': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1158:3: note: in expansion of macro 'assert' 1158 | assert (fileType == NULL || strlen(fileType) > 0) ; | ^~~~~~ ONElib.c: In function 'addProvenance': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1760:3: note: in expansion of macro 'assert' 1760 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'addReference': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1811:3: note: in expansion of macro 'assert' 1811 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'writeHeader': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1885:3: note: in expansion of macro 'assert' 1885 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1886:3: note: in expansion of macro 'assert' 1886 | assert (vf->line == 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1887:3: note: in expansion of macro 'assert' 1887 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'oneWriteLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2029:3: note: in expansion of macro 'assert' 2029 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2030:3: note: in expansion of macro 'assert' 2030 | assert (!vf->isFinal || !isalpha(t)) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2033:3: note: in expansion of macro 'assert' 2033 | assert (li) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2040:7: note: in expansion of macro 'assert' 2040 | { assert (listLen >= 0) ; | ^~~~~~ ONElib.c: In function 'oneFileClose': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2488:3: note: in expansion of macro 'assert' 2488 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'intGet': ONElib.c:3490:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3490 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3491:9: note: here 3491 | case 1: *pval = *(I64*)(u+1) & 0x0000000000ffff ; return 3 ; | ^~~~ ONElib.c:3502:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3502 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3503:9: note: here 3503 | case 1: *pval = *(I64*)(u+1) | 0xffffffffffff0000 ; return 3 ; | ^~~~ ONElib.c:3488:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 3488 | switch (u[0] & 0x07) | ^~~~~~ ONElib.c:3499:5: note: here 3499 | case 4: | ^~~~ ONElib.c: In function 'ltfRead': ONElib.c:3564:10: warning: 'val' may be used uninitialized [-Wmaybe-uninitialized] 3564 | return val ; | ^~~ ONElib.c:3544:7: note: 'val' was declared here 3544 | I64 val ; | ^~~ ONElib.c: In function 'oneFileOpenWriteFrom': ONElib.c:395:33: warning: '%ld' directive writing between 1 and 19 bytes into a region of size between 7 and 25 [-Wformat-overflow=] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~ In function 'oneSchemaCreateDynamic', inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: ONElib.c:395:20: note: directive argument in the range [0, 9223372036854775805] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ONElib.c:22: In function 'sprintf', inlined from 'oneSchemaCreateDynamic' at ONElib.c:395:5, inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 or more bytes (assuming 47) into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ONElib.c: In function 'oneFileOpenWriteFrom': ONElib.c:395:33: warning: '%ld' directive writing between 1 and 19 bytes into a region of size between 7 and 25 [-Wformat-overflow=] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~ In function 'oneSchemaCreateDynamic', inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: ONElib.c:395:20: note: directive argument in the range [0, 9223372036854775805] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ONElib.c:22: In function 'sprintf', inlined from 'oneSchemaCreateDynamic' at ONElib.c:395:5, inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 or more bytes (assuming 47) into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_auto_install make -j12 install DESTDIR=/build/reproducible-path/daligner-1.0\+git20240119.335105d/debian/daligner AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' install -d /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin install daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LA2ONE LAcheck ONE2LA /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin make[2]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' mkdir -p /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/share/man/man1 for command in /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin/*; \ do \ if [ $(basename $command) != daligner ] ; \ then \ ln -s daligner.1 \ /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/share/man/man1/$(basename $command).1 ; \ fi; \ done make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'daligner' in '../daligner_1.0+git20240119.335105d-3_arm64.deb'. dpkg-deb: building package 'daligner-dbgsym' in '../daligner-dbgsym_1.0+git20240119.335105d-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../daligner_1.0+git20240119.335105d-3_arm64.buildinfo dpkg-genchanges --build=binary -O../daligner_1.0+git20240119.335105d-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2314927 and its subdirectories I: Current time: Wed Dec 24 09:53:31 -12 2025 I: pbuilder-time-stamp: 1766613211 Thu Nov 21 15:30:34 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Thu Nov 21 15:30:34 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Thu Nov 21 15:30:34 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Thu Nov 21 15:30:34 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-Ma8Fro' ==================================================================================== Wed Dec 24 21:53:35 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "2 daligner trixie /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z 1.0+git20240119.335105d-3" as arguments. Wed Dec 24 21:53:35 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-o33K64Be" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Dec 24 21:53:35 UTC 2025 I: Downloading source for trixie/daligner=1.0+git20240119.335105d-3 Reading package lists... NOTICE: 'daligner' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/daligner.git Please use: git clone https://salsa.debian.org/med-team/daligner.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 137 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (dsc) [2287 B] Get:2 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (tar) [128 kB] Get:3 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (diff) [6660 B] Fetched 137 kB in 0s (6147 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'daligner' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/daligner.git Please use: git clone https://salsa.debian.org/med-team/daligner.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 137 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (dsc) [2287 B] Get:2 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (tar) [128 kB] Get:3 http://deb.debian.org/debian trixie/main daligner 1.0+git20240119.335105d-3 (diff) [6660 B] Fetched 137 kB in 0s (6147 kB/s) Download complete and in download only mode ============================================================================= Re-Building daligner in trixie on arm64 on codethink01-arm64 now. Date: Wed Dec 24 21:53:35 GMT 2025 Date UTC: Wed Dec 24 21:53:36 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/pbuilderrc_MCry + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' daligner = debian-installer -o daligner = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' daligner = u-boot ']' + case "${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.XzNRJF8z/pbuilderrc_MCry --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.XzNRJF8z/b2 --logfile b2/build.log daligner_1.0+git20240119.335105d-3.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: Thu Dec 25 11:53:36 +14 2025 I: pbuilder-time-stamp: 1766613216 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [daligner_1.0+git20240119.335105d-3.dsc] I: copying [./daligner_1.0+git20240119.335105d.orig.tar.xz] I: copying [./daligner_1.0+git20240119.335105d-3.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Jul 3 20:48:16 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./daligner_1.0+git20240119.335105d-3.dsc: no acceptable signature found dpkg-source: info: extracting daligner in daligner-1.0+git20240119.335105d dpkg-source: info: unpacking daligner_1.0+git20240119.335105d.orig.tar.xz dpkg-source: info: unpacking daligner_1.0+git20240119.335105d-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cflags.patch dpkg-source: info: applying lddflags.patch dpkg-source: info: applying destdir-install.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying cppflags.patch dpkg-source: info: applying fix-missing-include.patch dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/61656/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. 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 Dec 24 21:53 /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/61656/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/61656/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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=c2a0d5750b834c88bde20acb8b5e1adf LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=61656 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.XzNRJF8z/pbuilderrc_MCry --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.XzNRJF8z/b2 --logfile b2/build.log daligner_1.0+git20240119.335105d-3.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/61656/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20087 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. 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 77.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Fetched 19.4 MB in 0s (70.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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/61656/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/61656/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/daligner-1.0+git20240119.335105d/ && 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 > ../daligner_1.0+git20240119.335105d-3_source.changes dpkg-buildpackage: info: source package daligner dpkg-buildpackage: info: source version 1.0+git20240119.335105d-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' rm -f daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LA2ONE LAcheck ONE2LA rm -fr *.dSYM rm -f daligner.tar.gz make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o daligner daligner.c filter.c lsd.sort.c align.c DB.c QV.c -lpthread -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o HPC.daligner HPC.daligner.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAsort LAsort.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAmerge LAmerge.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAsplit LAsplit.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAcat LAcat.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAshow LAshow.c align.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LA2ONE LA2ONE.c align.c DB.c QV.c ONElib.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o LAcheck LAcheck.c align.c DB.c QV.c -lm -Wl,-z,relro -Wl,-z,now cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/daligner-1.0+git20240119.335105d=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o ONE2LA ONE2LA.c align.c DB.c QV.c ONElib.c -lm -Wl,-z,relro -Wl,-z,now LAshow.c: In function 'main': LAshow.c:415:36: warning: variable 'lhalf' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~~ LAshow.c:415:30: warning: variable 'seen' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~ LAshow.c:415:23: warning: variable 'match' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~~ LAshow.c:415:16: warning: variable 'blast' set but not used [-Wunused-but-set-variable] 415 | int blast, match, seen, lhalf, rhalf; | ^~~~~ ONE2LA.c: In function 'main': ONE2LA.c:30:20: warning: variable 'small' set but not used [-Wunused-but-set-variable] 30 | int tspace, small, tbytes; | ^~~~~ LAshow.c:743:5: warning: 'bmap' may be used uninitialized [-Wmaybe-uninitialized] 743 | free(bmap); | ^~~~~~~~~~ LAshow.c:55:11: note: 'bmap' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~ LAshow.c:549:25: warning: 'blen' may be used uninitialized [-Wmaybe-uninitialized] 549 | blens = blen[bread]; | ^ LAshow.c:55:18: note: 'blen' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~ LAshow.c:588:40: warning: 'bctg' may be used uninitialized [-Wmaybe-uninitialized] 588 | printf(".%0*d",bc_wide,bctg[bread]+1); | ^ LAshow.c:55:25: note: 'bctg' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~ LAshow.c:448:19: warning: 'nbscaff' may be used uninitialized [-Wmaybe-uninitialized] 448 | { br_wide = Number_Digits((int64) nbscaff); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:55:31: note: 'nbscaff' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~~~~ LAshow.c:449:19: warning: 'bmaxlen' may be used uninitialized [-Wmaybe-uninitialized] 449 | bi_wide = Number_Digits((int64) bmaxlen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:55:40: note: 'bmaxlen' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~~~~ LAshow.c:450:19: warning: 'bctgmax' may be used uninitialized [-Wmaybe-uninitialized] 450 | bc_wide = Number_Digits((int64) bctgmax); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:55:49: note: 'bctgmax' was declared here 55 | int *bmap, *blen, *bctg, nbscaff, bmaxlen, bctgmax; | ^~~~~~~ LAshow.c:744:3: warning: 'amap' may be used uninitialized [-Wmaybe-uninitialized] 744 | free(amap); | ^~~~~~~~~~ LAshow.c:54:11: note: 'amap' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~ LAshow.c:541:25: warning: 'alen' may be used uninitialized [-Wmaybe-uninitialized] 541 | alens = alen[aread]; | ^ LAshow.c:54:18: note: 'alen' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~ LAshow.c:581:40: warning: 'actg' may be used uninitialized [-Wmaybe-uninitialized] 581 | printf(".%0*d",ac_wide,actg[aread]+1); | ^ LAshow.c:54:25: note: 'actg' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~ LAshow.c:439:19: warning: 'nascaff' may be used uninitialized [-Wmaybe-uninitialized] 439 | { ar_wide = Number_Digits((int64) nascaff); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:54:31: note: 'nascaff' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~~~~ LAshow.c:440:19: warning: 'amaxlen' may be used uninitialized [-Wmaybe-uninitialized] 440 | ai_wide = Number_Digits((int64) amaxlen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:54:40: note: 'amaxlen' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~~~~ LAshow.c:441:19: warning: 'actgmax' may be used uninitialized [-Wmaybe-uninitialized] 441 | ac_wide = Number_Digits((int64) actgmax); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LAshow.c:54:49: note: 'actgmax' was declared here 54 | int *amap, *alen, *actg, nascaff, amaxlen, actgmax; | ^~~~~~~ filter.c: In function 'report_thread': filter.c:2155:23: warning: suggest braces around empty body in an 'else' statement [-Wempty-body] 2155 | ; | ^ ONElib.c: In function 'oneSchemaCreateDynamic': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:392:3: note: in expansion of macro 'assert' 392 | assert (fileType && strlen(fileType) > 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:393:3: note: in expansion of macro 'assert' 393 | assert (!subType || strlen(subType) > 0) ; | ^~~~~~ ONElib.c: In function 'readBuf': ONElib.c:616:40: warning: comparison is always false due to limited range of data type [-Wtype-limits] 616 | if (isspace(x) || x == '\0' || x == EOF) | ^~ ONElib.c: In function 'readString': ONElib.c:664:32: warning: comparison is always false due to limited range of data type [-Wtype-limits] 664 | if (*cp == '\n' || *cp == EOF) | ^~ ONElib.c: In function 'readFlush': ONElib.c:695:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 695 | if (x == EOF) | ^~ ONElib.c: In function 'oneReadLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:945:3: note: in expansion of macro 'assert' 945 | assert (!vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:946:3: note: in expansion of macro 'assert' 946 | assert (!vf->isFinal) ; | ^~~~~~ ONElib.c: In function 'oneFileOpenRead': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1158:3: note: in expansion of macro 'assert' 1158 | assert (fileType == NULL || strlen(fileType) > 0) ; | ^~~~~~ ONElib.c: In function 'addProvenance': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1760:3: note: in expansion of macro 'assert' 1760 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'addReference': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1811:3: note: in expansion of macro 'assert' 1811 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'writeHeader': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1885:3: note: in expansion of macro 'assert' 1885 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1886:3: note: in expansion of macro 'assert' 1886 | assert (vf->line == 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1887:3: note: in expansion of macro 'assert' 1887 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'oneWriteLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2029:3: note: in expansion of macro 'assert' 2029 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2030:3: note: in expansion of macro 'assert' 2030 | assert (!vf->isFinal || !isalpha(t)) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2033:3: note: in expansion of macro 'assert' 2033 | assert (li) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2040:7: note: in expansion of macro 'assert' 2040 | { assert (listLen >= 0) ; | ^~~~~~ ONElib.c: In function 'oneFileClose': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2488:3: note: in expansion of macro 'assert' 2488 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'intGet': ONElib.c:3490:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3490 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3491:9: note: here 3491 | case 1: *pval = *(I64*)(u+1) & 0x0000000000ffff ; return 3 ; | ^~~~ ONElib.c:3502:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3502 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3503:9: note: here 3503 | case 1: *pval = *(I64*)(u+1) | 0xffffffffffff0000 ; return 3 ; | ^~~~ ONElib.c:3488:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 3488 | switch (u[0] & 0x07) | ^~~~~~ ONElib.c:3499:5: note: here 3499 | case 4: | ^~~~ ONElib.c: In function 'ltfRead': ONElib.c:3564:10: warning: 'val' may be used uninitialized [-Wmaybe-uninitialized] 3564 | return val ; | ^~~ ONElib.c:3544:7: note: 'val' was declared here 3544 | I64 val ; | ^~~ ONElib.c: In function 'oneSchemaCreateDynamic': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:392:3: note: in expansion of macro 'assert' 392 | assert (fileType && strlen(fileType) > 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:393:3: note: in expansion of macro 'assert' 393 | assert (!subType || strlen(subType) > 0) ; | ^~~~~~ ONElib.c: In function 'readBuf': ONElib.c:616:40: warning: comparison is always false due to limited range of data type [-Wtype-limits] 616 | if (isspace(x) || x == '\0' || x == EOF) | ^~ ONElib.c: In function 'readString': ONElib.c:664:32: warning: comparison is always false due to limited range of data type [-Wtype-limits] 664 | if (*cp == '\n' || *cp == EOF) | ^~ ONElib.c: In function 'readFlush': ONElib.c:695:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 695 | if (x == EOF) | ^~ ONElib.c: In function 'oneReadLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:945:3: note: in expansion of macro 'assert' 945 | assert (!vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:946:3: note: in expansion of macro 'assert' 946 | assert (!vf->isFinal) ; | ^~~~~~ ONElib.c: In function 'oneFileOpenRead': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1158:3: note: in expansion of macro 'assert' 1158 | assert (fileType == NULL || strlen(fileType) > 0) ; | ^~~~~~ ONElib.c: In function 'addProvenance': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1760:3: note: in expansion of macro 'assert' 1760 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'addReference': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1811:3: note: in expansion of macro 'assert' 1811 | assert (!vf->isHeaderOut) ; | ^~~~~~ ONElib.c: In function 'writeHeader': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1885:3: note: in expansion of macro 'assert' 1885 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1886:3: note: in expansion of macro 'assert' 1886 | assert (vf->line == 0) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:1887:3: note: in expansion of macro 'assert' 1887 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'oneWriteLine': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2029:3: note: in expansion of macro 'assert' 2029 | assert (vf->isWrite) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2030:3: note: in expansion of macro 'assert' 2030 | assert (!vf->isFinal || !isalpha(t)) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2033:3: note: in expansion of macro 'assert' 2033 | assert (li) ; | ^~~~~~ ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2040:7: note: in expansion of macro 'assert' 2040 | { assert (listLen >= 0) ; | ^~~~~~ ONElib.c: In function 'oneFileClose': ONElib.c:37:19: warning: statement with no effect [-Wunused-value] 37 | #define assert(x) 0 | ^ ONElib.c:2488:3: note: in expansion of macro 'assert' 2488 | assert (vf->share >= 0) ; | ^~~~~~ ONElib.c: In function 'intGet': ONElib.c:3490:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3490 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3491:9: note: here 3491 | case 1: *pval = *(I64*)(u+1) & 0x0000000000ffff ; return 3 ; | ^~~~ ONElib.c:3502:17: warning: this statement may fall through [-Wimplicit-fallthrough=] 3502 | case 0: die ("int packing error") ; | ^~~~~~~~~~~~~~~~~~~~~~~~~ ONElib.c:3503:9: note: here 3503 | case 1: *pval = *(I64*)(u+1) | 0xffffffffffff0000 ; return 3 ; | ^~~~ ONElib.c:3488:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 3488 | switch (u[0] & 0x07) | ^~~~~~ ONElib.c:3499:5: note: here 3499 | case 4: | ^~~~ ONElib.c: In function 'ltfRead': ONElib.c:3564:10: warning: 'val' may be used uninitialized [-Wmaybe-uninitialized] 3564 | return val ; | ^~~ ONElib.c:3544:7: note: 'val' was declared here 3544 | I64 val ; | ^~~ ONElib.c: In function 'oneFileOpenWriteFrom': ONElib.c:395:33: warning: '%ld' directive writing between 1 and 19 bytes into a region of size between 7 and 25 [-Wformat-overflow=] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~ In function 'oneSchemaCreateDynamic', inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: ONElib.c:395:20: note: directive argument in the range [0, 9223372036854775805] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ONElib.c:22: In function 'sprintf', inlined from 'oneSchemaCreateDynamic' at ONElib.c:395:5, inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 or more bytes (assuming 47) into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ONElib.c: In function 'oneFileOpenWriteFrom': ONElib.c:395:33: warning: '%ld' directive writing between 1 and 19 bytes into a region of size between 7 and 25 [-Wformat-overflow=] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~ In function 'oneSchemaCreateDynamic', inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: ONElib.c:395:20: note: directive argument in the range [0, 9223372036854775805] 395 | sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ; | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ONElib.c:22: In function 'sprintf', inlined from 'oneSchemaCreateDynamic' at ONElib.c:395:5, inlined from 'oneFileOpenWriteFrom' at ONElib.c:1657:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 11 or more bytes (assuming 47) into a destination of size 32 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_auto_install make -j12 install DESTDIR=/build/reproducible-path/daligner-1.0\+git20240119.335105d/debian/daligner AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' install -d /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin install daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LA2ONE LAcheck ONE2LA /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin make[2]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' mkdir -p /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/share/man/man1 for command in /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/bin/*; \ do \ if [ $(basename $command) != daligner ] ; \ then \ ln -s daligner.1 \ /build/reproducible-path/daligner-1.0+git20240119.335105d/debian/daligner/usr/share/man/man1/$(basename $command).1 ; \ fi; \ done make[1]: Leaving directory '/build/reproducible-path/daligner-1.0+git20240119.335105d' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'daligner-dbgsym' in '../daligner-dbgsym_1.0+git20240119.335105d-3_arm64.deb'. dpkg-deb: building package 'daligner' in '../daligner_1.0+git20240119.335105d-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../daligner_1.0+git20240119.335105d-3_arm64.buildinfo dpkg-genchanges --build=binary -O../daligner_1.0+git20240119.335105d-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/61656/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/61656/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/61656 and its subdirectories I: Current time: Thu Dec 25 11:54:59 +14 2025 + false + set +x I: pbuilder-time-stamp: 1766613299 Wed Dec 24 21:54:59 UTC 2025 I: Signing ./b2/daligner_1.0+git20240119.335105d-3_arm64.buildinfo as daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc Wed Dec 24 21:54:59 UTC 2025 I: Signed ./b2/daligner_1.0+git20240119.335105d-3_arm64.buildinfo as ./b2/daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc Wed Dec 24 21:54:59 UTC 2025 - build #2 for daligner/trixie/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Wed Dec 24 21:54:59 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-o33K64Be, removing. /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z: total 60 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 15:30 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 15:32 b2 -rw-r--r-- 1 jenkins jenkins 2287 Jul 3 20:55 daligner_1.0+git20240119.335105d-3.dsc -rw------- 1 jenkins jenkins 46934 Nov 21 15:30 rbuildlog.dvxg5w6 /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/b1: total 2000 -rw-r--r-- 1 jenkins jenkins 43142 Nov 21 15:30 build.log -rw-r--r-- 1 jenkins jenkins 1743336 Nov 21 15:30 daligner-dbgsym_1.0+git20240119.335105d-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 6660 Nov 21 15:30 daligner_1.0+git20240119.335105d-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2287 Nov 21 15:30 daligner_1.0+git20240119.335105d-3.dsc -rw-r--r-- 1 jenkins jenkins 5094 Nov 21 15:30 daligner_1.0+git20240119.335105d-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5976 Nov 21 15:30 daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1666 Nov 21 15:30 daligner_1.0+git20240119.335105d-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 212472 Nov 21 15:30 daligner_1.0+git20240119.335105d-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 1501 Nov 21 15:30 daligner_1.0+git20240119.335105d-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/b2: total 1996 -rw-r--r-- 1 jenkins jenkins 45066 Nov 21 15:32 build.log -rw-r--r-- 1 jenkins jenkins 1743336 Nov 21 15:32 daligner-dbgsym_1.0+git20240119.335105d-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 6660 Nov 21 15:32 daligner_1.0+git20240119.335105d-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2287 Nov 21 15:32 daligner_1.0+git20240119.335105d-3.dsc -rw-r--r-- 1 jenkins jenkins 5094 Nov 21 15:32 daligner_1.0+git20240119.335105d-3_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 5976 Nov 21 15:32 daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1666 Nov 21 15:32 daligner_1.0+git20240119.335105d-3_arm64.changes -rw-r--r-- 1 jenkins jenkins 212472 Nov 21 15:32 daligner_1.0+git20240119.335105d-3_arm64.deb -rw-r--r-- 1 jenkins jenkins 1501 Nov 21 15:32 daligner_1.0+git20240119.335105d-3_source.changes Thu Nov 21 15:32:00 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Thu Nov 21 15:32:01 UTC 2024 I: daligner_1.0+git20240119.335105d-3_arm64.changes: Format: 1.8 Date: Wed, 03 Jul 2024 22:45:58 +0200 Source: daligner Binary: daligner daligner-dbgsym Architecture: arm64 Version: 1.0+git20240119.335105d-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: daligner - local alignment discovery between long nucleotide sequencing read Closes: 1074900 Changes: daligner (1.0+git20240119.335105d-3) unstable; urgency=medium . * d/control: declare compliance to standards version 4.7.0. * gcc-14.patch: fix build failure with gcc-14. (Closes: #1074900) Checksums-Sha1: e97ddcb0a4c8c017d388ebb00dc36bf05e11b119 1743336 daligner-dbgsym_1.0+git20240119.335105d-3_arm64.deb 72240b446931fae7e5c5fa3ac750713f1adc503f 5094 daligner_1.0+git20240119.335105d-3_arm64.buildinfo fdb217316649efb685e3fb244e8b7fa019f698f9 212472 daligner_1.0+git20240119.335105d-3_arm64.deb Checksums-Sha256: 12404d0ae667effa9a0aaaa9a38fd5fb1d1f5d8d0cef7bab661cee7f761c4c7c 1743336 daligner-dbgsym_1.0+git20240119.335105d-3_arm64.deb 7a4e20fab6c4986c48ab217dab0179c49cdbea778cfb389b31df89b5ded03159 5094 daligner_1.0+git20240119.335105d-3_arm64.buildinfo 8b5c2183019580ad3feaea066e407222ff2817be99ccc7ac7d1fac821b47b051 212472 daligner_1.0+git20240119.335105d-3_arm64.deb Files: e84153253d97010745dd51f8044a9585 1743336 debug optional daligner-dbgsym_1.0+git20240119.335105d-3_arm64.deb ad319b2c28470456295b1b2167d3ddec 5094 science optional daligner_1.0+git20240119.335105d-3_arm64.buildinfo 8cb4a9eff23c39f6746cdaa94c7fb2b9 212472 science optional daligner_1.0+git20240119.335105d-3_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/daligner_1.0+git20240119.335105d-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/daligner_1.0+git20240119.335105d-3.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/daligner_1.0+git20240119.335105d-3.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/daligner_1.0+git20240119.335105d-3.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/arm64/daligner_1.0+git20240119.335105d-3_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/daligner_1.0+git20240119.335105d-3.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-21 15:30:33.091958562 +0000 +++ b2/build.log 2024-11-21 15:32:00.404025623 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Dec 24 09:52:54 -12 2025 -I: pbuilder-time-stamp: 1766613174 +I: Current time: Thu Dec 25 11:53:36 +14 2025 +I: pbuilder-time-stamp: 1766613216 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying gcc-14.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2314927/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/61656/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +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 Dec 24 21:53 /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/61656/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/61656/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='0481c53b68cb4bff9c484c70d12b4fd7' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2314927' - PS1='# ' - PS2='> ' + INVOCATION_ID=c2a0d5750b834c88bde20acb8b5e1adf + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=61656 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.XzNRJF8z/pbuilderrc_NE9P --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.XzNRJF8z/b1 --logfile b1/build.log daligner_1.0+git20240119.335105d-3.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.XzNRJF8z/pbuilderrc_MCry --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.XzNRJF8z/b2 --logfile b2/build.log daligner_1.0+git20240119.335105d-3.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2314927/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/61656/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -144,7 +176,7 @@ Get: 27 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] -Fetched 19.4 MB in 0s (123 MB/s) +Fetched 19.4 MB in 0s (70.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20087 files and directories currently installed.) @@ -275,7 +307,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/daligner-1.0+git20240119.335105d/ && 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 > ../daligner_1.0+git20240119.335105d-3_source.changes +I: user script /srv/workspace/pbuilder/61656/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/61656/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/daligner-1.0+git20240119.335105d/ && 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 > ../daligner_1.0+git20240119.335105d-3_source.changes dpkg-buildpackage: info: source package daligner dpkg-buildpackage: info: source version 1.0+git20240119.335105d-3 dpkg-buildpackage: info: source distribution unstable @@ -760,8 +796,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'daligner' in '../daligner_1.0+git20240119.335105d-3_arm64.deb'. dpkg-deb: building package 'daligner-dbgsym' in '../daligner-dbgsym_1.0+git20240119.335105d-3_arm64.deb'. +dpkg-deb: building package 'daligner' in '../daligner_1.0+git20240119.335105d-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../daligner_1.0+git20240119.335105d-3_arm64.buildinfo dpkg-genchanges --build=binary -O../daligner_1.0+git20240119.335105d-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -769,12 +805,14 @@ 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/61656/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/61656/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/2314927 and its subdirectories -I: Current time: Wed Dec 24 09:53:31 -12 2025 -I: pbuilder-time-stamp: 1766613211 +I: removing directory /srv/workspace/pbuilder/61656 and its subdirectories +I: Current time: Thu Dec 25 11:54:59 +14 2025 +I: pbuilder-time-stamp: 1766613299 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/daligner_1.0+git20240119.335105d-3.diff: 67.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/daligner_1.0+git20240119.335105d-3.diff.gz b2/build.log: 81.7% -- replaced with stdout Compressing the 1st log... b1/build.log: 82.4% -- replaced with stdout Thu Nov 21 15:32:02 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_daligner_trixie_arm64_1732203122 + touch /var/log/reproducible-builds/diffoscope_stamp_daligner_trixie_arm64_1732203122 + RESULT=0 + systemd-run '--description=diffoscope on daligner/1.0+git20240119.335105d-3 in trixie/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_5-69481 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z --run-session -c jenkins-reproducible-trixie-diffoscope-5fc31fc6-ba4e-47f2-a055-61c23ae71fe6 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/dbd-tmp-uxUi8zL ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/daligner_1.0+git20240119.335105d-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/daligner_1.0+git20240119.335105d-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/daligner_1.0+git20240119.335105d-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/b1/daligner_1.0+git20240119.335105d-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/b2/daligner_1.0+git20240119.335105d-3_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_5-69481.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/daligner_1.0+git20240119.335105d-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/daligner_1.0+git20240119.335105d-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/daligner_1.0+git20240119.335105d-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/b1/daligner_1.0+git20240119.335105d-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.XzNRJF8z/b2/daligner_1.0+git20240119.335105d-3_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.351s) 0.351s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.032s) 0.032s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 655ms CPU time consumed: 656ms _ _ _ __| | __ _| (_) __ _ _ __ ___ _ __ / _` |/ _` | | |/ _` | '_ \ / _ \ '__| | (_| | (_| | | | (_| | | | | __/ | \__,_|\__,_|_|_|\__, |_| |_|\___|_| |___/ Thu Nov 21 15:32:03 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 21 15:32:03 UTC 2024 I: daligner from trixie built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-21 15:32:04] INFO: Starting at 2024-11-21 15:32:04.025626 [2024-11-21 15:32:04] INFO: Generating the pages of 1 package(s) [2024-11-21 15:32:04] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/arm64/daligner didn't produce a buildlog, even though it has been built. [2024-11-21 15:32:04] INFO: Finished at 2024-11-21 15:32:04.507410, took: 0:00:00.481792 Thu Nov 21 15:32:04 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/arm64/daligner.html Thu Nov 21 15:32:04 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 21 15:32:04 UTC 2024 I: Submitting 8.0K b1/daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc https://buildinfo.debian.net/72240b446931fae7e5c5fa3ac750713f1adc503f/daligner_1.0+git20240119.335105d-3_arm64 Thu Nov 21 15:32:05 UTC 2024 I: Submitting 8.0K b2/daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc https://buildinfo.debian.net/50243dbd1437f876364301252fa2fcc8535a2911/daligner_1.0+git20240119.335105d-3_arm64 Thu Nov 21 15:32:06 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 21 15:32:06 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 21 15:32:06 UTC 2024 I: Removing signed daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc files: removed './b1/daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc' removed './b2/daligner_1.0+git20240119.335105d-3_arm64.buildinfo.asc' 1732203126 arm64 trixie daligner Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/daligner_1.0+git20240119.335105d-3.rbuild.log: 79.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/arm64/daligner_1.0+git20240119.335105d-3.rbuild.log.gz [2024-11-21 15:32:06] INFO: Starting at 2024-11-21 15:32:06.462242 [2024-11-21 15:32:06] INFO: Generating the pages of 1 package(s) [2024-11-21 15:32:06] INFO: Finished at 2024-11-21 15:32:06.901559, took: 0:00:00.439324 All cleanup done. Thu Nov 21 15:32:07 UTC 2024 - total duration: 0h 2m 16s. Thu Nov 21 15:32:07 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-gACYQRM9, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2min 19.294s CPU time consumed: 7.012s