Running as unit: rb-build-amd64_34-36750.service ==================================================================================== Sun Nov 24 09:44:09 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_34) on jenkins, called using "infom02-amd64 infom01-amd64" as arguments. Sun Nov 24 09:44:09 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-fXriezKO" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Nov 24 09:44:09 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Sun Nov 24 09:44:09 UTC 2024 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-K25mBK' Sun Nov 24 09:44:10 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Sun Nov 24 09:44:10 UTC 2024 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-8T1ps4' ok, let's check if readseq is building anywhere yet… ok, readseq is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of readseq in unstable on amd64 on jenkins now. 1st build will be done on infom02-amd64.debian.net. 2nd build will be done on infom01-amd64.debian.net. ============================================================================= Sun Nov 24 09:44:30 UTC 2024 I: starting to build readseq/unstable/amd64 on jenkins on '2024-11-24 09:44' Sun Nov 24 09:44:30 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_34/36750/console.log 1732441470 amd64 unstable readseq Sun Nov 24 09:44:30 UTC 2024 I: Downloading source for unstable/readseq=1-15 --2024-11-24 09:44:30-- http://deb.debian.org/debian/pool/main/r/readseq/readseq_1-15.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2069 (2.0K) [text/prs.lines.tag] Saving to: ‘readseq_1-15.dsc’ 0K .. 100% 261M=0s 2024-11-24 09:44:30 (261 MB/s) - ‘readseq_1-15.dsc’ saved [2069/2069] --2024-11-24 09:44:30-- http://deb.debian.org/debian/pool/main/r/readseq/readseq_1-15.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2069 (2.0K) [text/prs.lines.tag] Saving to: ‘readseq_1-15.dsc’ 0K .. 100% 261M=0s 2024-11-24 09:44:30 (261 MB/s) - ‘readseq_1-15.dsc’ saved [2069/2069] Sun Nov 24 09:44:30 UTC 2024 I: readseq_1-15.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: readseq Binary: readseq Architecture: any Version: 1-15 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://iubio.bio.indiana.edu/soft/molbio/readseq/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/readseq Vcs-Git: https://salsa.debian.org/med-team/readseq.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), ncbi-tools-dev Package-List: readseq deb science optional arch=any Checksums-Sha1: 474839186eec28f650ac89a33829673fa40c3bbb 54557 readseq_1.orig.tar.gz 05bd01a71c6861ae69ab5ac0a1d50d05da31b4e6 18120 readseq_1-15.debian.tar.xz Checksums-Sha256: b704d7a12c5d834390f3ed4233f1409c5f1ed53b0b9accf5ab632a513de1183c 54557 readseq_1.orig.tar.gz bef33c029eb0de6a7ea7d4844a2c8dee0acdc3562b8d74b830d84a73d3156226 18120 readseq_1-15.debian.tar.xz Files: 3973daff73375953369c31c5c1661699 54557 readseq_1.orig.tar.gz d9f89d7ecb8cfc662de77713a983685b 18120 readseq_1-15.debian.tar.xz Dgit: 9185439b5da210185b66a337e4a830b7828ffb1a debian archive/debian/1-15 https://git.dgit.debian.org/readseq -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmXzav0UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdr0Kw/+MhTjbVEzG2p1xd1TpucgukAIqZFb QGkVIlvgBQGan/K3DOKwT78vd/2uoFzzZBjkEEZDpp32ir/AQmg9U/0Q8fPgjiXx UlbQM9jGTlSUganGzvSmOLCX95ZeZpZnn6NU6SFHNBnOEHRgg08Y/U6PG9ehOlsw el/bAGGuCrbRm9/ye824Edr8NEaRyv5rblWPJc7LBqGRsHgG6Pwy4U9PmbVQzwwT 97AHkEv9/v5qKkWQ6pFdbOz0OYJxH49S9JbaUykGi3xXqthUjKU+gIemhkpQ+cJM 0NGzia6ycqFh8Dh8CPa8pBeHGBHa4dZUqOKCmOtC5J1CFDLnxRh+zTxuhh3jb8LW x3nivg1YBovqSP6F7fICWVOMj0Blud9SnLDR8BFkzwhHG9WP8mZcPlvQmBUigT/r lEvfRqUha5tE1VrXHqgRcify/OoO12LLVJmCQdBnHwFlQo8K3tDM28M0F/B8uTlS +QtbSOfdt7Pou1UjEHFqs07JjjLoCUTdz0Wph0flSZ4kcvx1BG6ewAJwDpciiv4z 6VNeh8MXkw5f6ErVE1O+QwZaNfrwVaCMSwZ9n0AmW9fwU4EssNPEkzFxxWfepxPf Z40mSX03wGcjHk8RJ3p/bFpFjLSelUnMUeCBb7lGJCiLowa5ft2P64IvjVB+xy7p YVgqHf27jVjpG9g= =S4uy -----END PGP SIGNATURE----- Sun Nov 24 09:44:30 UTC 2024 I: Checking whether the package is not for us Sun Nov 24 09:44:30 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Sun Nov 24 09:44:30 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Sun Nov 24 09:44:30 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom02-amd64.debian.net is marked as down. Sun Nov 24 09:44:30 UTC 2024 - checking via ssh if infom02-amd64.debian.net is up. removed '/tmp/read-only-fs-test-6Faq4d' ==================================================================================== Sat Dec 27 16:07:32 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom02-amd64, called using "1 readseq unstable /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs 1-15" as arguments. Sat Dec 27 16:07:32 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-r6nKn3IX" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Dec 27 16:07:32 UTC 2025 I: Downloading source for unstable/readseq=1-15 Reading package lists... NOTICE: 'readseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/readseq.git Please use: git clone https://salsa.debian.org/med-team/readseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 74.7 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main readseq 1-15 (dsc) [2069 B] Get:2 http://deb.debian.org/debian unstable/main readseq 1-15 (tar) [54.6 kB] Get:3 http://deb.debian.org/debian unstable/main readseq 1-15 (diff) [18.1 kB] Fetched 74.7 kB in 0s (664 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'readseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/readseq.git Please use: git clone https://salsa.debian.org/med-team/readseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 74.7 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main readseq 1-15 (dsc) [2069 B] Get:2 http://deb.debian.org/debian unstable/main readseq 1-15 (tar) [54.6 kB] Get:3 http://deb.debian.org/debian unstable/main readseq 1-15 (diff) [18.1 kB] Fetched 74.7 kB in 0s (664 kB/s) Download complete and in download only mode ============================================================================= Building readseq in unstable on amd64 on infom02-amd64 now. Date: Sat Dec 27 16:07:32 UTC 2025 Date UTC: Sat Dec 27 16:07:32 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: Sat Dec 27 04:07:32 -12 2025 I: pbuilder-time-stamp: 1766851652 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [readseq_1-15.dsc] I: copying [./readseq_1.orig.tar.gz] I: copying [./readseq_1-15.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Mar 14 21:24:13 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 ./readseq_1-15.dsc: no acceptable signature found dpkg-source: info: extracting readseq in readseq-1 dpkg-source: info: unpacking readseq_1.orig.tar.gz dpkg-source: info: unpacking readseq_1-15.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 20-Formats.patch dpkg-source: info: applying 20-Makefile.patch dpkg-source: info: applying 30-arb-code-patches.patch dpkg-source: info: applying 552830.patch dpkg-source: info: applying gcc-4.6_format-security.patch dpkg-source: info: applying enable_tests.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying buffer_overflow.patch dpkg-source: info: applying fix_tests.patch dpkg-source: info: applying fix-gets.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1038449/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='5c08173a049143f6a7b1097c23dfed9d' 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='1038449' 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.UjEt1rBs/pbuilderrc_RRtD --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b1 --logfile b1/build.log readseq_1-15.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' I: uname -a Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1038449/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), ncbi-tools-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on ncbi-tools-dev; however: Package ncbi-tools-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} 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} libncbi6-dev{a} libncbi6t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} ncbi-data{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 ncbi-tools-bin wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 33.0 MB of archives. After unpacking 142 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libncbi6t64 amd64 6.1.20170106+dfsg2-5 [4103 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libncbi6-dev amd64 6.1.20170106+dfsg2-5 [5538 kB] Fetched 33.0 MB in 1s (30.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.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 ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/readseq-1/ && 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 > ../readseq_1-15_source.changes dpkg-buildpackage: info: source package readseq dpkg-buildpackage: info: source version 1-15 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/readseq-1' rm -f *.o core test.* readseq make[1]: Leaving directory '/build/reproducible-path/readseq-1' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/readseq-1' dh_clean rm -f readseq make[1]: Leaving directory '/build/reproducible-path/readseq-1' 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/readseq-1' Compiling readseq with NCBI toolkit support and ARB patches gcc -o readseq -I/usr/include/ncbi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/readseq-1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -DNCBI -I/usr/include/ncbi -DARB readseq.c ureadseq.c ureadasn.c -lncbi -lncbiobj -lncbicdr -lncbiacc -lncbitool -lncbimmdb -lncbiid1 -lnetcli -lm -Wl,-z,relro -Wl,-z,now readseq.c: In function 'formatstr': readseq.c:267:41: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 267 | case kASNseqset : return formats[kASN1-1]; | ~~~~~~~^~~~~~~~~ readseq.c:269:45: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 269 | case kPhylipSequential: return formats[kPhylip-1]; | ~~~~~~~^~~~~~~~~~~ readseq.c:273:22: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 273 | else return formats[format-1]; | ~~~~~~~^~~~~~~~~~ readseq.c: In function 'Nlm_Main': readseq.c:936:33: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 936 | sprintf( stemp,"%s_%d", oname, whichSeq); | ~^ ~~~~~~~~ | | | | int long int | %ld readseq.c:938:48: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 938 | fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp); | ~^ ~~~~~~~~ | | | | int long int | %ld readseq.c:980:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | int | %ld 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~~~ | | | long int readseq.c:980:51: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | int | %ld 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~ | | | long int readseq.c:980:65: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | unsigned int | %lX 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~~~ | | | long unsigned int readseq.c:998:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); | ~^ ~ | | | | int long int | %ld readseq.c:998:56: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:999:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 999 | else fprintf(foo," %d %d YF\n", i, seqlen); | ~^ ~ | | | | int long int | %ld readseq.c:999:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 999 | else fprintf(foo," %d %d YF\n", i, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1117:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ | ~^ | | | int | %ld 1118 | cp, seqlen, timestr, checkall); | ~~~~~~ | | | long int readseq.c:1117:55: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long unsigned int' [-Wformat=] 1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ | ~^ | | | int | %ld 1118 | cp, seqlen, timestr, checkall); | ~~~~~~~~ | | | long unsigned int readseq.c:1133:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1133 | if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1134:28: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1134 | else fprintf(foo," %d %d YF\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1158:49: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1158 | fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c: In function 'seqFileFormatFp': ureadseq.c:1535:19: warning: format '%d' expects argument of type 'int *', but argument 3 has type 'long int *' [-Wformat=] 1535 | sscanf( sp, "%d%d", &nspp, &nlen); | ~^ ~~~~~ | | | | int * long int * | %ld ureadseq.c:1535:21: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long int *' [-Wformat=] 1535 | sscanf( sp, "%d%d", &nspp, &nlen); | ~^ ~~~~~ | | | | int * long int * | %ld ureadseq.c: In function 'writeSeq': ureadseq.c:1784:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1784 | sprintf(numform, "%d", seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1813:43: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1813 | fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1814:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1814:48: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1828:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1828:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1838:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1838 | for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j); | ~~~^ ~ | | | | | long int | int | %10ld ureadseq.c:1848:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1848:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1857:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1857:41: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1858:37: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1858 | fprintf(outf,"SQ %d BP\n", seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1869:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1869:58: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); | ~^ ~~~~~~~~ | | | | int long unsigned int | %ld ureadseq.c:1878:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1878:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1884:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1884:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1915:53: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1915 | fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1937:41: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); | ~~^ ~~~~~~ | | | | int long int | %6ld ureadseq.c:1937:53: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); | ~~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %8lX ureadseq.c:1954:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); | ~~^ ~~~~~~ | | | | int long int | %6ld ureadseq.c:1954:54: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); | ~~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %8lX ureadseq.c:1960:40: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", | ~~^ | | | int | %6ld 1961 | idword, seqlen, checksum); | ~~~~~~ | | | long int ureadseq.c:1960:52: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", | ~~^ | | | int | %5ld 1961 | idword, seqlen, checksum); | ~~~~~~~~ | | | long unsigned int ureadseq.c:1972:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1972:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1979:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1979 | fprintf(outf,"%4d %-60s\n",seqlen,seqname); | ~~^ ~~~~~~ | | | | int long int | %4ld ureadseq.c:2002:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:2002:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:2043:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 2043 | if (numline==1) fprintf(outf,"%-9d ",i+1); | ~~~^ ~~~ | | | | int long int | %-9ld ureadseq.c: In function 'readPAUPinterleaved': ureadseq.c:213:22: warning: '%s' directive writing up to 255 bytes into a region of size between 246 and 251 [-Wformat-overflow=] 213 | sprintf(si, " %d) %s\n", V->nseq, s); | ^~ In function 'addinfo', inlined from 'readPAUPinterleaved' at ureadseq.c:813:13: ureadseq.c:213:3: note: 'sprintf' output between 7 and 267 bytes into a destination of size 256 213 | sprintf(si, " %d) %s\n", V->nseq, s); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadseq.c: In function 'writeSeq': ureadseq.c:2007:45: warning: '%d' directive writing between 1 and 6 bytes into a region of size between 2 and 7 [-Wformat-overflow=] 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~ ureadseq.c:2007:39: note: directive argument in the range [-32768, 32767] 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~~~~~~~~~~ ureadseq.c:2007:21: note: 'sprintf' output between 7 and 17 bytes into a destination of size 10 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c: In function 'listASNSeqs': ureadasn.c:189:24: warning: passing argument 1 of 'AsnIoOpen' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 189 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit; | ^~~~~~~~ In file included from /usr/include/ncbi/ncbi.h:57, from ureadasn.c:13: /usr/include/ncbi/asn.h:384:54: note: expected 'Nlm_CharPtr' {aka 'char *'} but argument is of type 'const char *' 384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode)); /usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro 'PROTO' 192 | #define PROTO(x) x /* Prototypes are acceptable */ | ^ ureadasn.c: In function 'readASNSeq': ureadasn.c:261:24: warning: passing argument 1 of 'AsnIoOpen' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 261 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit; | ^~~~~~~~ /usr/include/ncbi/asn.h:384:54: note: expected 'Nlm_CharPtr' {aka 'char *'} but argument is of type 'const char *' 384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode)); /usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro 'PROTO' 192 | #define PROTO(x) x /* Prototypes are acceptable */ | ^ ureadasn.c:262:31: warning: 'fgets' writing 255 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=] 262 | for (i=0; ifp); /* this may mess up asn routines... */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c:241:15: note: destination object 'stemp' of size 200 241 | char *seq, stemp[200]; | ^~~~~ In file included from ureadasn.c:8: /usr/include/stdio.h:654:14: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 654 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ /usr/bin/ld: /tmp/ccH3OOUS.o: in function `Nlm_Main': ././readseq.c:783:(.text+0x1767): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[1]: Leaving directory '/build/reproducible-path/readseq-1' dh_auto_test make -j12 test make[1]: Entering directory '/build/reproducible-path/readseq-1' Test for general read/write of all chars: ./readseq -p alphabet.std -otest.alpha diff test.alpha alphabet.std Test for valid format conversions: ./readseq -v -p -f=ig nucleic.std -otest.ig Sequence 1, length= 228, checksum= 1B5655D0, format= 20. Vienna, id= nucleic/amino test ./readseq -v -p -f=gb test.ig -otest.gb Sequence 1, length= 228, checksum= 1B5655D0, format= 1. IG/Stanford, id= nucleic/amino ./readseq -v -p -f=nbrf test.gb -otest.nbrf Sequence 1, length= 228, checksum= 1B5655D0, format= 2. GenBank/GB, id= nucleic/amino 228 bp ./readseq -v -p -f=embl test.nbrf -otest.embl Sequence 1, length= 228, checksum= 1B5655D0, format= 3. NBRF, id= nucleic/amino ./readseq -v -p -f=gcg test.embl -otest.gcg Sequence 1, length= 228, checksum= 1B5655D0, format= 4. EMBL, id= nucleic/amino ./readseq -v -p -f=strider test.gcg -otest.strider Sequence 1, length= 228, checksum= 1B5655D0, format= 5. GCG, id= nucleic/amino ./readseq -v -p -f=fitch test.strider -otest.fitch Sequence 1, length= 228, checksum= 1B5655D0, format= 6. DNAStrider, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=fasta test.fitch -otest.fasta Sequence 1, length= 228, checksum= 1B5655D0, format= 7. Fitch, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=pir test.fasta -otest.pir Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=ig test.pir -otest.ig-b Sequence 1, length= 228, checksum= 1B5655D0, format= 14. PIR/CODATA, id= nucleic/amino, diff test.ig test.ig-b 1,2c1,2 < ;nucleic/amino test, 228 bases, 1B5655D0 checksum. < nucleic/amino --- > ;nucleic/amino, , 228 bases, 1B5655D0 checksum. > nucleic/amino, make[1]: [Makefile:70: test] Error 1 (ignored) Test for multiple-sequence format conversions: ./readseq -p -f=ig multi.std -otest.m-ig ./readseq -p -f=gb test.m-ig -otest.m-gb ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf ./readseq -p -f=embl test.m-nbrf -otest.m-embl ./readseq -p -f=fasta test.m-embl -otest.m-fasta ./readseq -p -f=pir test.m-fasta -otest.m-pir ./readseq -p -f=msf test.m-pir -otest.m-msf ./readseq -p -f=paup test.m-msf -otest.m-paup ./readseq -p -f=ig test.m-paup -otest.m-ig-b diff test.m-ig test.m-ig-b 1,2c1,2 < ;acarr58sst , 183 bases, 64754A4D checksum. < acarr58sst --- > ;acarr58ss, 183 bases, 64754A4D checksum. > acarr58ss 7c7 < ;amgrrbst , 183 bases, C886D2FB checksum. --- > ;amgrrbst, 183 bases, C886D2FB checksum. 13c13 < ;bmorrbst , 183 bases, 3E9C23D6 checksum. --- > ;bmorrbst, 183 bases, 3E9C23D6 checksum. 19c19 < ;crerrbst , 183 bases, AC88A337 checksum. --- > ;crerrbst, 183 bases, AC88A337 checksum. 25,26c25,26 < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. < ddirr58sst --- > ;ddirr58ss, 183 bases, 1E3D23B8 checksum. > ddirr58ss make[1]: [Makefile:82: test] Error 1 (ignored) Expect differences in the header lines due to different format headers. If any sequence lines differ, or if the checksums differ, there is a problem. ---------------------- To clean up test files, command me: make clean make[1]: Leaving directory '/build/reproducible-path/readseq-1' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/readseq/ make -j12 install DESTDIR=/build/reproducible-path/readseq-1/debian/readseq AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/readseq-1' install readseq /build/reproducible-path/readseq-1/debian/readseq/usr/bin install *.std /build/reproducible-path/readseq-1/debian/readseq/usr/share/doc/readseq/tests install Makefile /build/reproducible-path/readseq-1/debian/readseq/usr/share/doc/readseq/tests make[1]: Leaving directory '/build/reproducible-path/readseq-1' dh_install 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'readseq' in '../readseq_1-15_amd64.deb'. dpkg-deb: building package 'readseq-dbgsym' in '../readseq-dbgsym_1-15_amd64.deb'. dpkg-genbuildinfo --build=binary -O../readseq_1-15_amd64.buildinfo dpkg-genchanges --build=binary -O../readseq_1-15_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/1038449 and its subdirectories I: Current time: Sat Dec 27 04:08:31 -12 2025 I: pbuilder-time-stamp: 1766851711 Sat Dec 27 16:08:31 UTC 2025 I: Signing ./b1/readseq_1-15_amd64.buildinfo as readseq_1-15_amd64.buildinfo.asc Sat Dec 27 16:08:31 UTC 2025 I: Signed ./b1/readseq_1-15_amd64.buildinfo as ./b1/readseq_1-15_amd64.buildinfo.asc Sat Dec 27 16:08:31 UTC 2025 - build #1 for readseq/unstable/amd64 on infom02-amd64 done. Starting cleanup. All cleanup done. Sat Dec 27 16:08:31 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-r6nKn3IX, removing. /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 24 09:45 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 24 09:44 b2 -rw------- 1 jenkins jenkins 3156 Nov 24 09:44 rbuildlog.Nagoqsp -rw-r--r-- 1 jenkins jenkins 2069 Mar 14 2024 readseq_1-15.dsc /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b1: total 220 -rw-r--r-- 1 jenkins jenkins 52424 Nov 24 09:45 build.log -rw-r--r-- 1 jenkins jenkins 65268 Nov 24 09:45 readseq-dbgsym_1-15_amd64.deb -rw-r--r-- 1 jenkins jenkins 18120 Nov 24 09:45 readseq_1-15.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2069 Nov 24 09:45 readseq_1-15.dsc -rw-r--r-- 1 jenkins jenkins 5235 Nov 24 09:45 readseq_1-15_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6117 Nov 24 09:45 readseq_1-15_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1444 Nov 24 09:45 readseq_1-15_amd64.changes -rw-r--r-- 1 jenkins jenkins 55740 Nov 24 09:45 readseq_1-15_amd64.deb -rw-r--r-- 1 jenkins jenkins 1323 Nov 24 09:45 readseq_1-15_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b2: total 0 Sun Nov 24 09:45:32 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Dec 27 04:07:32 -12 2025 I: pbuilder-time-stamp: 1766851652 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [readseq_1-15.dsc] I: copying [./readseq_1.orig.tar.gz] I: copying [./readseq_1-15.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Mar 14 21:24:13 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 ./readseq_1-15.dsc: no acceptable signature found dpkg-source: info: extracting readseq in readseq-1 dpkg-source: info: unpacking readseq_1.orig.tar.gz dpkg-source: info: unpacking readseq_1-15.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 20-Formats.patch dpkg-source: info: applying 20-Makefile.patch dpkg-source: info: applying 30-arb-code-patches.patch dpkg-source: info: applying 552830.patch dpkg-source: info: applying gcc-4.6_format-security.patch dpkg-source: info: applying enable_tests.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying buffer_overflow.patch dpkg-source: info: applying fix_tests.patch dpkg-source: info: applying fix-gets.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1038449/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='5c08173a049143f6a7b1097c23dfed9d' 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='1038449' 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.UjEt1rBs/pbuilderrc_RRtD --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b1 --logfile b1/build.log readseq_1-15.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' I: uname -a Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1038449/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), ncbi-tools-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on ncbi-tools-dev; however: Package ncbi-tools-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} 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} libncbi6-dev{a} libncbi6t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} ncbi-data{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 ncbi-tools-bin wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 33.0 MB of archives. After unpacking 142 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libncbi6t64 amd64 6.1.20170106+dfsg2-5 [4103 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libncbi6-dev amd64 6.1.20170106+dfsg2-5 [5538 kB] Fetched 33.0 MB in 1s (30.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.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:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_amd64.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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Setting up libicu72:amd64 (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:amd64 (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:amd64 (0.192-4) ... Setting up libncbi6t64:amd64 (6.1.20170106+dfsg2-5) ... 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:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/readseq-1/ && 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 > ../readseq_1-15_source.changes dpkg-buildpackage: info: source package readseq dpkg-buildpackage: info: source version 1-15 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/readseq-1' rm -f *.o core test.* readseq make[1]: Leaving directory '/build/reproducible-path/readseq-1' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/readseq-1' dh_clean rm -f readseq make[1]: Leaving directory '/build/reproducible-path/readseq-1' 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/readseq-1' Compiling readseq with NCBI toolkit support and ARB patches gcc -o readseq -I/usr/include/ncbi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/readseq-1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -DNCBI -I/usr/include/ncbi -DARB readseq.c ureadseq.c ureadasn.c -lncbi -lncbiobj -lncbicdr -lncbiacc -lncbitool -lncbimmdb -lncbiid1 -lnetcli -lm -Wl,-z,relro -Wl,-z,now readseq.c: In function 'formatstr': readseq.c:267:41: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 267 | case kASNseqset : return formats[kASN1-1]; | ~~~~~~~^~~~~~~~~ readseq.c:269:45: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 269 | case kPhylipSequential: return formats[kPhylip-1]; | ~~~~~~~^~~~~~~~~~~ readseq.c:273:22: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 273 | else return formats[format-1]; | ~~~~~~~^~~~~~~~~~ readseq.c: In function 'Nlm_Main': readseq.c:936:33: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 936 | sprintf( stemp,"%s_%d", oname, whichSeq); | ~^ ~~~~~~~~ | | | | int long int | %ld readseq.c:938:48: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 938 | fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp); | ~^ ~~~~~~~~ | | | | int long int | %ld readseq.c:980:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | int | %ld 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~~~ | | | long int readseq.c:980:51: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | int | %ld 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~ | | | long int readseq.c:980:65: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | unsigned int | %lX 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~~~ | | | long unsigned int readseq.c:998:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); | ~^ ~ | | | | int long int | %ld readseq.c:998:56: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:999:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 999 | else fprintf(foo," %d %d YF\n", i, seqlen); | ~^ ~ | | | | int long int | %ld readseq.c:999:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 999 | else fprintf(foo," %d %d YF\n", i, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1117:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ | ~^ | | | int | %ld 1118 | cp, seqlen, timestr, checkall); | ~~~~~~ | | | long int readseq.c:1117:55: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long unsigned int' [-Wformat=] 1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ | ~^ | | | int | %ld 1118 | cp, seqlen, timestr, checkall); | ~~~~~~~~ | | | long unsigned int readseq.c:1133:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1133 | if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1134:28: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1134 | else fprintf(foo," %d %d YF\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1158:49: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1158 | fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c: In function 'seqFileFormatFp': ureadseq.c:1535:19: warning: format '%d' expects argument of type 'int *', but argument 3 has type 'long int *' [-Wformat=] 1535 | sscanf( sp, "%d%d", &nspp, &nlen); | ~^ ~~~~~ | | | | int * long int * | %ld ureadseq.c:1535:21: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long int *' [-Wformat=] 1535 | sscanf( sp, "%d%d", &nspp, &nlen); | ~^ ~~~~~ | | | | int * long int * | %ld ureadseq.c: In function 'writeSeq': ureadseq.c:1784:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1784 | sprintf(numform, "%d", seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1813:43: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1813 | fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1814:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1814:48: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1828:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1828:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1838:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1838 | for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j); | ~~~^ ~ | | | | | long int | int | %10ld ureadseq.c:1848:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1848:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1857:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1857:41: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1858:37: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1858 | fprintf(outf,"SQ %d BP\n", seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1869:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1869:58: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); | ~^ ~~~~~~~~ | | | | int long unsigned int | %ld ureadseq.c:1878:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1878:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1884:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1884:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1915:53: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1915 | fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1937:41: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); | ~~^ ~~~~~~ | | | | int long int | %6ld ureadseq.c:1937:53: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); | ~~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %8lX ureadseq.c:1954:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); | ~~^ ~~~~~~ | | | | int long int | %6ld ureadseq.c:1954:54: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); | ~~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %8lX ureadseq.c:1960:40: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", | ~~^ | | | int | %6ld 1961 | idword, seqlen, checksum); | ~~~~~~ | | | long int ureadseq.c:1960:52: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", | ~~^ | | | int | %5ld 1961 | idword, seqlen, checksum); | ~~~~~~~~ | | | long unsigned int ureadseq.c:1972:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1972:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1979:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1979 | fprintf(outf,"%4d %-60s\n",seqlen,seqname); | ~~^ ~~~~~~ | | | | int long int | %4ld ureadseq.c:2002:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:2002:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:2043:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 2043 | if (numline==1) fprintf(outf,"%-9d ",i+1); | ~~~^ ~~~ | | | | int long int | %-9ld ureadseq.c: In function 'readPAUPinterleaved': ureadseq.c:213:22: warning: '%s' directive writing up to 255 bytes into a region of size between 246 and 251 [-Wformat-overflow=] 213 | sprintf(si, " %d) %s\n", V->nseq, s); | ^~ In function 'addinfo', inlined from 'readPAUPinterleaved' at ureadseq.c:813:13: ureadseq.c:213:3: note: 'sprintf' output between 7 and 267 bytes into a destination of size 256 213 | sprintf(si, " %d) %s\n", V->nseq, s); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadseq.c: In function 'writeSeq': ureadseq.c:2007:45: warning: '%d' directive writing between 1 and 6 bytes into a region of size between 2 and 7 [-Wformat-overflow=] 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~ ureadseq.c:2007:39: note: directive argument in the range [-32768, 32767] 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~~~~~~~~~~ ureadseq.c:2007:21: note: 'sprintf' output between 7 and 17 bytes into a destination of size 10 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c: In function 'listASNSeqs': ureadasn.c:189:24: warning: passing argument 1 of 'AsnIoOpen' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 189 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit; | ^~~~~~~~ In file included from /usr/include/ncbi/ncbi.h:57, from ureadasn.c:13: /usr/include/ncbi/asn.h:384:54: note: expected 'Nlm_CharPtr' {aka 'char *'} but argument is of type 'const char *' 384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode)); /usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro 'PROTO' 192 | #define PROTO(x) x /* Prototypes are acceptable */ | ^ ureadasn.c: In function 'readASNSeq': ureadasn.c:261:24: warning: passing argument 1 of 'AsnIoOpen' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 261 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit; | ^~~~~~~~ /usr/include/ncbi/asn.h:384:54: note: expected 'Nlm_CharPtr' {aka 'char *'} but argument is of type 'const char *' 384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode)); /usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro 'PROTO' 192 | #define PROTO(x) x /* Prototypes are acceptable */ | ^ ureadasn.c:262:31: warning: 'fgets' writing 255 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=] 262 | for (i=0; ifp); /* this may mess up asn routines... */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c:241:15: note: destination object 'stemp' of size 200 241 | char *seq, stemp[200]; | ^~~~~ In file included from ureadasn.c:8: /usr/include/stdio.h:654:14: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 654 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ /usr/bin/ld: /tmp/ccH3OOUS.o: in function `Nlm_Main': ././readseq.c:783:(.text+0x1767): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[1]: Leaving directory '/build/reproducible-path/readseq-1' dh_auto_test make -j12 test make[1]: Entering directory '/build/reproducible-path/readseq-1' Test for general read/write of all chars: ./readseq -p alphabet.std -otest.alpha diff test.alpha alphabet.std Test for valid format conversions: ./readseq -v -p -f=ig nucleic.std -otest.ig Sequence 1, length= 228, checksum= 1B5655D0, format= 20. Vienna, id= nucleic/amino test ./readseq -v -p -f=gb test.ig -otest.gb Sequence 1, length= 228, checksum= 1B5655D0, format= 1. IG/Stanford, id= nucleic/amino ./readseq -v -p -f=nbrf test.gb -otest.nbrf Sequence 1, length= 228, checksum= 1B5655D0, format= 2. GenBank/GB, id= nucleic/amino 228 bp ./readseq -v -p -f=embl test.nbrf -otest.embl Sequence 1, length= 228, checksum= 1B5655D0, format= 3. NBRF, id= nucleic/amino ./readseq -v -p -f=gcg test.embl -otest.gcg Sequence 1, length= 228, checksum= 1B5655D0, format= 4. EMBL, id= nucleic/amino ./readseq -v -p -f=strider test.gcg -otest.strider Sequence 1, length= 228, checksum= 1B5655D0, format= 5. GCG, id= nucleic/amino ./readseq -v -p -f=fitch test.strider -otest.fitch Sequence 1, length= 228, checksum= 1B5655D0, format= 6. DNAStrider, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=fasta test.fitch -otest.fasta Sequence 1, length= 228, checksum= 1B5655D0, format= 7. Fitch, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=pir test.fasta -otest.pir Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=ig test.pir -otest.ig-b Sequence 1, length= 228, checksum= 1B5655D0, format= 14. PIR/CODATA, id= nucleic/amino, diff test.ig test.ig-b 1,2c1,2 < ;nucleic/amino test, 228 bases, 1B5655D0 checksum. < nucleic/amino --- > ;nucleic/amino, , 228 bases, 1B5655D0 checksum. > nucleic/amino, make[1]: [Makefile:70: test] Error 1 (ignored) Test for multiple-sequence format conversions: ./readseq -p -f=ig multi.std -otest.m-ig ./readseq -p -f=gb test.m-ig -otest.m-gb ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf ./readseq -p -f=embl test.m-nbrf -otest.m-embl ./readseq -p -f=fasta test.m-embl -otest.m-fasta ./readseq -p -f=pir test.m-fasta -otest.m-pir ./readseq -p -f=msf test.m-pir -otest.m-msf ./readseq -p -f=paup test.m-msf -otest.m-paup ./readseq -p -f=ig test.m-paup -otest.m-ig-b diff test.m-ig test.m-ig-b 1,2c1,2 < ;acarr58sst , 183 bases, 64754A4D checksum. < acarr58sst --- > ;acarr58ss, 183 bases, 64754A4D checksum. > acarr58ss 7c7 < ;amgrrbst , 183 bases, C886D2FB checksum. --- > ;amgrrbst, 183 bases, C886D2FB checksum. 13c13 < ;bmorrbst , 183 bases, 3E9C23D6 checksum. --- > ;bmorrbst, 183 bases, 3E9C23D6 checksum. 19c19 < ;crerrbst , 183 bases, AC88A337 checksum. --- > ;crerrbst, 183 bases, AC88A337 checksum. 25,26c25,26 < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. < ddirr58sst --- > ;ddirr58ss, 183 bases, 1E3D23B8 checksum. > ddirr58ss make[1]: [Makefile:82: test] Error 1 (ignored) Expect differences in the header lines due to different format headers. If any sequence lines differ, or if the checksums differ, there is a problem. ---------------------- To clean up test files, command me: make clean make[1]: Leaving directory '/build/reproducible-path/readseq-1' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/readseq/ make -j12 install DESTDIR=/build/reproducible-path/readseq-1/debian/readseq AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/readseq-1' install readseq /build/reproducible-path/readseq-1/debian/readseq/usr/bin install *.std /build/reproducible-path/readseq-1/debian/readseq/usr/share/doc/readseq/tests install Makefile /build/reproducible-path/readseq-1/debian/readseq/usr/share/doc/readseq/tests make[1]: Leaving directory '/build/reproducible-path/readseq-1' dh_install 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'readseq' in '../readseq_1-15_amd64.deb'. dpkg-deb: building package 'readseq-dbgsym' in '../readseq-dbgsym_1-15_amd64.deb'. dpkg-genbuildinfo --build=binary -O../readseq_1-15_amd64.buildinfo dpkg-genchanges --build=binary -O../readseq_1-15_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/1038449 and its subdirectories I: Current time: Sat Dec 27 04:08:31 -12 2025 I: pbuilder-time-stamp: 1766851711 Sun Nov 24 09:45:33 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Sun Nov 24 09:45:33 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Sun Nov 24 09:45:33 UTC 2024 - checking /var/lib/jenkins/offline_nodes if infom01-amd64.debian.net is marked as down. Sun Nov 24 09:45:33 UTC 2024 - checking via ssh if infom01-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Xz1aR0' ==================================================================================== Sun Nov 24 09:45:34 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on infom01-amd64, called using "2 readseq unstable /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs 1-15" as arguments. Sun Nov 24 09:45:34 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-yvJ9CMYp" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Nov 24 09:45:34 UTC 2024 I: Downloading source for unstable/readseq=1-15 Reading package lists... NOTICE: 'readseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/readseq.git Please use: git clone https://salsa.debian.org/med-team/readseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 74.7 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main readseq 1-15 (dsc) [2069 B] Get:2 http://deb.debian.org/debian unstable/main readseq 1-15 (tar) [54.6 kB] Get:3 http://deb.debian.org/debian unstable/main readseq 1-15 (diff) [18.1 kB] Fetched 74.7 kB in 0s (1039 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'readseq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/readseq.git Please use: git clone https://salsa.debian.org/med-team/readseq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 74.7 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main readseq 1-15 (dsc) [2069 B] Get:2 http://deb.debian.org/debian unstable/main readseq 1-15 (tar) [54.6 kB] Get:3 http://deb.debian.org/debian unstable/main readseq 1-15 (diff) [18.1 kB] Fetched 74.7 kB in 0s (1039 kB/s) Download complete and in download only mode ============================================================================= Re-Building readseq in unstable on amd64 on infom01-amd64 now. Date: Sun Nov 24 09:45:34 UTC 2024 Date UTC: Sun Nov 24 09:45:34 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/pbuilderrc_EsZR + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' readseq = debian-installer -o readseq = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' readseq = u-boot ']' + case "${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.UjEt1rBs/pbuilderrc_EsZR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b2 --logfile b2/build.log readseq_1-15.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 24 23:45:34 +14 2024 I: pbuilder-time-stamp: 1732441534 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [readseq_1-15.dsc] I: copying [./readseq_1.orig.tar.gz] I: copying [./readseq_1-15.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Mar 14 21:24:13 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 ./readseq_1-15.dsc: no acceptable signature found dpkg-source: info: extracting readseq in readseq-1 dpkg-source: info: unpacking readseq_1.orig.tar.gz dpkg-source: info: unpacking readseq_1-15.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 20-Formats.patch dpkg-source: info: applying 20-Makefile.patch dpkg-source: info: applying 30-arb-code-patches.patch dpkg-source: info: applying 552830.patch dpkg-source: info: applying gcc-4.6_format-security.patch dpkg-source: info: applying enable_tests.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying buffer_overflow.patch dpkg-source: info: applying fix_tests.patch dpkg-source: info: applying fix-gets.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1885245/tmp/hooks/D01_modify_environment starting debug: Running on infom01-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 24 09:45 /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/1885245/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1885245/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]="x86_64-pc-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=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=605ecefc84634f67a94a4b626a48d026 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1885245 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.UjEt1rBs/pbuilderrc_EsZR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b2 --logfile b2/build.log readseq_1-15.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' I: uname -a Linux i-capture-the-hostname 6.1.0-27-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1885245/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), ncbi-tools-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on ncbi-tools-dev; however: Package ncbi-tools-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} 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} libncbi6-dev{a} libncbi6t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} ncbi-data{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 ncbi-tools-bin wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 33.0 MB of archives. After unpacking 142 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libncbi6t64 amd64 6.1.20170106+dfsg2-5 [4103 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libncbi6-dev amd64 6.1.20170106+dfsg2-5 [5538 kB] Fetched 33.0 MB in 0s (87.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1885245/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1885245/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/readseq-1/ && 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 > ../readseq_1-15_source.changes dpkg-buildpackage: info: source package readseq dpkg-buildpackage: info: source version 1-15 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/readseq-1' rm -f *.o core test.* readseq make[1]: Leaving directory '/build/reproducible-path/readseq-1' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/readseq-1' dh_clean rm -f readseq make[1]: Leaving directory '/build/reproducible-path/readseq-1' 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/readseq-1' Compiling readseq with NCBI toolkit support and ARB patches gcc -o readseq -I/usr/include/ncbi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/readseq-1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -DNCBI -I/usr/include/ncbi -DARB readseq.c ureadseq.c ureadasn.c -lncbi -lncbiobj -lncbicdr -lncbiacc -lncbitool -lncbimmdb -lncbiid1 -lnetcli -lm -Wl,-z,relro -Wl,-z,now readseq.c: In function 'formatstr': readseq.c:267:41: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 267 | case kASNseqset : return formats[kASN1-1]; | ~~~~~~~^~~~~~~~~ readseq.c:269:45: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 269 | case kPhylipSequential: return formats[kPhylip-1]; | ~~~~~~~^~~~~~~~~~~ readseq.c:273:22: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 273 | else return formats[format-1]; | ~~~~~~~^~~~~~~~~~ readseq.c: In function 'Nlm_Main': readseq.c:936:33: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 936 | sprintf( stemp,"%s_%d", oname, whichSeq); | ~^ ~~~~~~~~ | | | | int long int | %ld readseq.c:938:48: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 938 | fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp); | ~^ ~~~~~~~~ | | | | int long int | %ld readseq.c:980:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | int | %ld 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~~~ | | | long int readseq.c:980:51: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | int | %ld 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~ | | | long int readseq.c:980:65: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | unsigned int | %lX 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~~~ | | | long unsigned int readseq.c:998:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); | ~^ ~ | | | | int long int | %ld readseq.c:998:56: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:999:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 999 | else fprintf(foo," %d %d YF\n", i, seqlen); | ~^ ~ | | | | int long int | %ld readseq.c:999:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 999 | else fprintf(foo," %d %d YF\n", i, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1117:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ | ~^ | | | int | %ld 1118 | cp, seqlen, timestr, checkall); | ~~~~~~ | | | long int readseq.c:1117:55: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long unsigned int' [-Wformat=] 1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ | ~^ | | | int | %ld 1118 | cp, seqlen, timestr, checkall); | ~~~~~~~~ | | | long unsigned int readseq.c:1133:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1133 | if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1134:28: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1134 | else fprintf(foo," %d %d YF\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1158:49: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1158 | fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c: In function 'seqFileFormatFp': ureadseq.c:1535:19: warning: format '%d' expects argument of type 'int *', but argument 3 has type 'long int *' [-Wformat=] 1535 | sscanf( sp, "%d%d", &nspp, &nlen); | ~^ ~~~~~ | | | | int * long int * | %ld ureadseq.c:1535:21: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long int *' [-Wformat=] 1535 | sscanf( sp, "%d%d", &nspp, &nlen); | ~^ ~~~~~ | | | | int * long int * | %ld ureadseq.c: In function 'writeSeq': ureadseq.c:1784:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1784 | sprintf(numform, "%d", seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1813:43: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1813 | fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1814:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1814:48: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1828:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1828:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1838:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1838 | for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j); | ~~~^ ~ | | | | | long int | int | %10ld ureadseq.c:1848:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1848:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1857:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1857:41: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1858:37: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1858 | fprintf(outf,"SQ %d BP\n", seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1869:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1869:58: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); | ~^ ~~~~~~~~ | | | | int long unsigned int | %ld ureadseq.c:1878:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1878:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1884:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1884:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1915:53: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1915 | fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1937:41: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); | ~~^ ~~~~~~ | | | | int long int | %6ld ureadseq.c:1937:53: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); | ~~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %8lX ureadseq.c:1954:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); | ~~^ ~~~~~~ | | | | int long int | %6ld ureadseq.c:1954:54: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); | ~~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %8lX ureadseq.c:1960:40: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", | ~~^ | | | int | %6ld 1961 | idword, seqlen, checksum); | ~~~~~~ | | | long int ureadseq.c:1960:52: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", | ~~^ | | | int | %5ld 1961 | idword, seqlen, checksum); | ~~~~~~~~ | | | long unsigned int ureadseq.c:1972:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1972:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1979:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1979 | fprintf(outf,"%4d %-60s\n",seqlen,seqname); | ~~^ ~~~~~~ | | | | int long int | %4ld ureadseq.c:2002:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:2002:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:2043:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 2043 | if (numline==1) fprintf(outf,"%-9d ",i+1); | ~~~^ ~~~ | | | | int long int | %-9ld ureadseq.c: In function 'readPAUPinterleaved': ureadseq.c:213:22: warning: '%s' directive writing up to 255 bytes into a region of size between 246 and 251 [-Wformat-overflow=] 213 | sprintf(si, " %d) %s\n", V->nseq, s); | ^~ In function 'addinfo', inlined from 'readPAUPinterleaved' at ureadseq.c:813:13: ureadseq.c:213:3: note: 'sprintf' output between 7 and 267 bytes into a destination of size 256 213 | sprintf(si, " %d) %s\n", V->nseq, s); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadseq.c: In function 'writeSeq': ureadseq.c:2007:45: warning: '%d' directive writing between 1 and 6 bytes into a region of size between 2 and 7 [-Wformat-overflow=] 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~ ureadseq.c:2007:39: note: directive argument in the range [-32768, 32767] 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~~~~~~~~~~ ureadseq.c:2007:21: note: 'sprintf' output between 7 and 17 bytes into a destination of size 10 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c: In function 'listASNSeqs': ureadasn.c:189:24: warning: passing argument 1 of 'AsnIoOpen' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 189 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit; | ^~~~~~~~ In file included from /usr/include/ncbi/ncbi.h:57, from ureadasn.c:13: /usr/include/ncbi/asn.h:384:54: note: expected 'Nlm_CharPtr' {aka 'char *'} but argument is of type 'const char *' 384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode)); /usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro 'PROTO' 192 | #define PROTO(x) x /* Prototypes are acceptable */ | ^ ureadasn.c: In function 'readASNSeq': ureadasn.c:261:24: warning: passing argument 1 of 'AsnIoOpen' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 261 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit; | ^~~~~~~~ /usr/include/ncbi/asn.h:384:54: note: expected 'Nlm_CharPtr' {aka 'char *'} but argument is of type 'const char *' 384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode)); /usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro 'PROTO' 192 | #define PROTO(x) x /* Prototypes are acceptable */ | ^ ureadasn.c:262:31: warning: 'fgets' writing 255 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=] 262 | for (i=0; ifp); /* this may mess up asn routines... */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c:241:15: note: destination object 'stemp' of size 200 241 | char *seq, stemp[200]; | ^~~~~ In file included from ureadasn.c:8: /usr/include/stdio.h:654:14: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 654 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ /usr/bin/ld: /tmp/cctF4Vfv.o: in function `Nlm_Main': ././readseq.c:783:(.text+0x1767): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[1]: Leaving directory '/build/reproducible-path/readseq-1' dh_auto_test make -j12 test make[1]: Entering directory '/build/reproducible-path/readseq-1' Test for general read/write of all chars: ./readseq -p alphabet.std -otest.alpha diff test.alpha alphabet.std Test for valid format conversions: ./readseq -v -p -f=ig nucleic.std -otest.ig Sequence 1, length= 228, checksum= 1B5655D0, format= 20. Vienna, id= nucleic/amino test ./readseq -v -p -f=gb test.ig -otest.gb Sequence 1, length= 228, checksum= 1B5655D0, format= 1. IG/Stanford, id= nucleic/amino ./readseq -v -p -f=nbrf test.gb -otest.nbrf Sequence 1, length= 228, checksum= 1B5655D0, format= 2. GenBank/GB, id= nucleic/amino 228 bp ./readseq -v -p -f=embl test.nbrf -otest.embl Sequence 1, length= 228, checksum= 1B5655D0, format= 3. NBRF, id= nucleic/amino ./readseq -v -p -f=gcg test.embl -otest.gcg Sequence 1, length= 228, checksum= 1B5655D0, format= 4. EMBL, id= nucleic/amino ./readseq -v -p -f=strider test.gcg -otest.strider Sequence 1, length= 228, checksum= 1B5655D0, format= 5. GCG, id= nucleic/amino ./readseq -v -p -f=fitch test.strider -otest.fitch Sequence 1, length= 228, checksum= 1B5655D0, format= 6. DNAStrider, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=fasta test.fitch -otest.fasta Sequence 1, length= 228, checksum= 1B5655D0, format= 7. Fitch, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=pir test.fasta -otest.pir Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=ig test.pir -otest.ig-b Sequence 1, length= 228, checksum= 1B5655D0, format= 14. PIR/CODATA, id= nucleic/amino, diff test.ig test.ig-b 1,2c1,2 < ;nucleic/amino test, 228 bases, 1B5655D0 checksum. < nucleic/amino --- > ;nucleic/amino, , 228 bases, 1B5655D0 checksum. > nucleic/amino, make[1]: [Makefile:70: test] Error 1 (ignored) Test for multiple-sequence format conversions: ./readseq -p -f=ig multi.std -otest.m-ig ./readseq -p -f=gb test.m-ig -otest.m-gb ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf ./readseq -p -f=embl test.m-nbrf -otest.m-embl ./readseq -p -f=fasta test.m-embl -otest.m-fasta ./readseq -p -f=pir test.m-fasta -otest.m-pir ./readseq -p -f=msf test.m-pir -otest.m-msf ./readseq -p -f=paup test.m-msf -otest.m-paup ./readseq -p -f=ig test.m-paup -otest.m-ig-b diff test.m-ig test.m-ig-b 1,2c1,2 < ;acarr58sst , 183 bases, 64754A4D checksum. < acarr58sst --- > ;acarr58ss, 183 bases, 64754A4D checksum. > acarr58ss 7c7 < ;amgrrbst , 183 bases, C886D2FB checksum. --- > ;amgrrbst, 183 bases, C886D2FB checksum. 13c13 < ;bmorrbst , 183 bases, 3E9C23D6 checksum. --- > ;bmorrbst, 183 bases, 3E9C23D6 checksum. 19c19 < ;crerrbst , 183 bases, AC88A337 checksum. --- > ;crerrbst, 183 bases, AC88A337 checksum. 25,26c25,26 < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. < ddirr58sst --- > ;ddirr58ss, 183 bases, 1E3D23B8 checksum. > ddirr58ss make[1]: [Makefile:82: test] Error 1 (ignored) Expect differences in the header lines due to different format headers. If any sequence lines differ, or if the checksums differ, there is a problem. ---------------------- To clean up test files, command me: make clean make[1]: Leaving directory '/build/reproducible-path/readseq-1' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/readseq/ make -j12 install DESTDIR=/build/reproducible-path/readseq-1/debian/readseq AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/readseq-1' install readseq /build/reproducible-path/readseq-1/debian/readseq/usr/bin install *.std /build/reproducible-path/readseq-1/debian/readseq/usr/share/doc/readseq/tests install Makefile /build/reproducible-path/readseq-1/debian/readseq/usr/share/doc/readseq/tests make[1]: Leaving directory '/build/reproducible-path/readseq-1' dh_install 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'readseq-dbgsym' in '../readseq-dbgsym_1-15_amd64.deb'. dpkg-deb: building package 'readseq' in '../readseq_1-15_amd64.deb'. dpkg-genbuildinfo --build=binary -O../readseq_1-15_amd64.buildinfo dpkg-genchanges --build=binary -O../readseq_1-15_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1885245/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1885245/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/1885245 and its subdirectories I: Current time: Sun Nov 24 23:46:16 +14 2024 I: pbuilder-time-stamp: 1732441576 + false + set +x Sun Nov 24 09:46:16 UTC 2024 I: Signing ./b2/readseq_1-15_amd64.buildinfo as readseq_1-15_amd64.buildinfo.asc Sun Nov 24 09:46:17 UTC 2024 I: Signed ./b2/readseq_1-15_amd64.buildinfo as ./b2/readseq_1-15_amd64.buildinfo.asc Sun Nov 24 09:46:17 UTC 2024 - build #2 for readseq/unstable/amd64 on infom01-amd64 done. Starting cleanup. All cleanup done. Sun Nov 24 09:46:17 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-yvJ9CMYp, removing. /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs: total 72 drwxr-xr-x 2 jenkins jenkins 4096 Nov 24 09:45 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 24 09:46 b2 -rw------- 1 jenkins jenkins 55869 Nov 24 09:45 rbuildlog.Nagoqsp -rw-r--r-- 1 jenkins jenkins 2069 Mar 14 2024 readseq_1-15.dsc /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b1: total 232 -rw-r--r-- 1 jenkins jenkins 52424 Nov 24 09:45 build.log -rw-r--r-- 1 jenkins jenkins 65268 Nov 24 09:45 readseq-dbgsym_1-15_amd64.deb -rw-r--r-- 1 jenkins jenkins 18120 Nov 24 09:45 readseq_1-15.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2069 Nov 24 09:45 readseq_1-15.dsc -rw-r--r-- 1 jenkins jenkins 5235 Nov 24 09:45 readseq_1-15_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6117 Nov 24 09:45 readseq_1-15_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1444 Nov 24 09:45 readseq_1-15_amd64.changes -rw-r--r-- 1 jenkins jenkins 55740 Nov 24 09:45 readseq_1-15_amd64.deb -rw-r--r-- 1 jenkins jenkins 1323 Nov 24 09:45 readseq_1-15_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b2: total 224 -rw-r--r-- 1 jenkins jenkins 54355 Nov 24 09:46 build.log -rw-r--r-- 1 jenkins jenkins 65268 Nov 24 09:46 readseq-dbgsym_1-15_amd64.deb -rw-r--r-- 1 jenkins jenkins 18120 Nov 24 09:46 readseq_1-15.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2069 Nov 24 09:46 readseq_1-15.dsc -rw-r--r-- 1 jenkins jenkins 5232 Nov 24 09:46 readseq_1-15_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 6114 Nov 24 09:46 readseq_1-15_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1444 Nov 24 09:46 readseq_1-15_amd64.changes -rw-r--r-- 1 jenkins jenkins 55740 Nov 24 09:46 readseq_1-15_amd64.deb -rw-r--r-- 1 jenkins jenkins 1323 Nov 24 09:46 readseq_1-15_source.changes Sun Nov 24 09:46:17 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Sun Nov 24 09:46:18 UTC 2024 I: readseq_1-15_amd64.changes: Format: 1.8 Date: Thu, 14 Mar 2024 22:07:41 +0100 Source: readseq Binary: readseq readseq-dbgsym Architecture: amd64 Version: 1-15 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: readseq - Conversion between sequence formats Closes: 1066478 Changes: readseq (1-15) unstable; urgency=medium . * Team upload. * fix-gets.patch: new: replace gets by fgets. (Closes: #1066478) * Remove unnecessary get-orig-source-target. * Update standards version to 4.6.2, no changes needed. Checksums-Sha1: 14a57a66288ffe5a6a8ef92f439ff8de72caf135 65268 readseq-dbgsym_1-15_amd64.deb 70dfda0be2c5ffab2ceebe3d01af866b9dbad3ff 5235 readseq_1-15_amd64.buildinfo 37f653af63b1bcd5b7a2be747f35b7e78facb68d 55740 readseq_1-15_amd64.deb Checksums-Sha256: ff52f2ea63b62269de40fc80dca0c34a066ee166f718bb51fdb4f2963a2cfeb5 65268 readseq-dbgsym_1-15_amd64.deb ae261b1504d9aef7242c7368c39ba539190f5bd407294cb5aedaf01cc5564043 5235 readseq_1-15_amd64.buildinfo 25bf3d42de1bf02e83ff4d13ac29725bd23ba6d812b4d11d19eaa47e79fcc520 55740 readseq_1-15_amd64.deb Files: 1fe1e2ab5b4f76dc416ea96a2ef29e00 65268 debug optional readseq-dbgsym_1-15_amd64.deb e48975a2c61937202996b04c95128098 5235 science optional readseq_1-15_amd64.buildinfo 312047a686cf6040725770775acbc7fd 55740 science optional readseq_1-15_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/readseq_1-15.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/readseq_1-15.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/readseq_1-15.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/readseq_1-15.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/readseq_1-15_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/readseq_1-15.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-24 09:45:32.503810191 +0000 +++ b2/build.log 2024-11-24 09:46:17.813765179 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Dec 27 04:07:32 -12 2025 -I: pbuilder-time-stamp: 1766851652 +I: Current time: Sun Nov 24 23:45:34 +14 2024 +I: pbuilder-time-stamp: 1732441534 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -37,51 +37,83 @@ dpkg-source: info: applying fix-gets.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1038449/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1885245/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 24 09:45 /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/1885245/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1885245/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='amd64' - 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]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='5c08173a049143f6a7b1097c23dfed9d' - 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='1038449' - PS1='# ' - PS2='> ' + INVOCATION_ID=605ecefc84634f67a94a4b626a48d026 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1885245 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.UjEt1rBs/pbuilderrc_RRtD --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b1 --logfile b1/build.log readseq_1-15.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' + 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.UjEt1rBs/pbuilderrc_EsZR --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b2 --logfile b2/build.log readseq_1-15.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' I: uname -a - Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1038449/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1885245/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -151,7 +183,7 @@ Get: 30 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libncbi6t64 amd64 6.1.20170106+dfsg2-5 [4103 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libncbi6-dev amd64 6.1.20170106+dfsg2-5 [5538 kB] -Fetched 33.0 MB in 1s (30.1 MB/s) +Fetched 33.0 MB in 0s (87.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19966 files and directories currently installed.) @@ -294,7 +326,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/readseq-1/ && 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 > ../readseq_1-15_source.changes +I: user script /srv/workspace/pbuilder/1885245/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1885245/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/readseq-1/ && 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 > ../readseq_1-15_source.changes dpkg-buildpackage: info: source package readseq dpkg-buildpackage: info: source version 1-15 dpkg-buildpackage: info: source distribution unstable @@ -696,7 +732,7 @@ /usr/include/stdio.h:654:14: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 654 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ -/usr/bin/ld: /tmp/ccH3OOUS.o: in function `Nlm_Main': +/usr/bin/ld: /tmp/cctF4Vfv.o: in function `Nlm_Main': ././readseq.c:783:(.text+0x1767): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make[1]: Leaving directory '/build/reproducible-path/readseq-1' dh_auto_test @@ -810,8 +846,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'readseq' in '../readseq_1-15_amd64.deb'. dpkg-deb: building package 'readseq-dbgsym' in '../readseq-dbgsym_1-15_amd64.deb'. +dpkg-deb: building package 'readseq' in '../readseq_1-15_amd64.deb'. dpkg-genbuildinfo --build=binary -O../readseq_1-15_amd64.buildinfo dpkg-genchanges --build=binary -O../readseq_1-15_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -819,12 +855,14 @@ 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/1885245/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1885245/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/1038449 and its subdirectories -I: Current time: Sat Dec 27 04:08:31 -12 2025 -I: pbuilder-time-stamp: 1766851711 +I: removing directory /srv/workspace/pbuilder/1885245 and its subdirectories +I: Current time: Sun Nov 24 23:46:16 +14 2024 +I: pbuilder-time-stamp: 1732441576 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/readseq_1-15.diff: 66.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/readseq_1-15.diff.gz b2/build.log: 81.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 82.0% -- replaced with stdout Sun Nov 24 09:46:19 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_readseq_unstable_amd64_1732441579 + touch /var/log/reproducible-builds/diffoscope_stamp_readseq_unstable_amd64_1732441579 + RESULT=0 + systemd-run '--description=diffoscope on readseq/1-15 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_34-36750 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs --run-session -c jenkins-reproducible-unstable-diffoscope-6d2c7731-a8b9-424a-9e4f-f6a53b91c3c6 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/dbd-tmp-Q4OKkt0 ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/readseq_1-15.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/readseq_1-15.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/readseq_1-15.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b1/readseq_1-15_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b2/readseq_1-15_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_34-36750.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/readseq_1-15.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/readseq_1-15.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/readseq_1-15.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b1/readseq_1-15_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.UjEt1rBs/b2/readseq_1-15_amd64.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: 0.388s) 0.388s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.018s) 0.018s 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: 762ms CPU time consumed: 756ms _ _ __ ___ __ _ __| |___ ___ __ _ | '__/ _ \/ _` |/ _` / __|/ _ \/ _` | | | | __/ (_| | (_| \__ \ __/ (_| | |_| \___|\__,_|\__,_|___/\___|\__, | |_| Sun Nov 24 09:46:21 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Sun Nov 24 09:46:21 UTC 2024 I: readseq from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-24 09:46:21] INFO: Starting at 2024-11-24 09:46:21.651718 [2024-11-24 09:46:21] INFO: Generating the pages of 1 package(s) [2024-11-24 09:46:22] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/readseq didn't produce a buildlog, even though it has been built. [2024-11-24 09:46:22] INFO: Finished at 2024-11-24 09:46:22.233638, took: 0:00:00.581928 Sun Nov 24 09:46:22 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/readseq.html Sun Nov 24 09:46:22 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Nov 24 09:46:22 UTC 2024 I: Submitting 8.0K b1/readseq_1-15_amd64.buildinfo.asc https://buildinfo.debian.net/70dfda0be2c5ffab2ceebe3d01af866b9dbad3ff/readseq_1-15_amd64 Sun Nov 24 09:46:23 UTC 2024 I: Submitting 8.0K b2/readseq_1-15_amd64.buildinfo.asc https://buildinfo.debian.net/74573e2d533f05f23fd5d11596a867ef3069af2f/readseq_1-15_amd64 Sun Nov 24 09:46:24 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Nov 24 09:46:24 UTC 2024 I: Done submitting .buildinfo files. Sun Nov 24 09:46:24 UTC 2024 I: Removing signed readseq_1-15_amd64.buildinfo.asc files: removed './b1/readseq_1-15_amd64.buildinfo.asc' removed './b2/readseq_1-15_amd64.buildinfo.asc' 1732441584 amd64 unstable readseq Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/readseq_1-15.rbuild.log: 79.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/readseq_1-15.rbuild.log.gz [2024-11-24 09:46:24] INFO: Starting at 2024-11-24 09:46:24.500995 [2024-11-24 09:46:24] INFO: Generating the pages of 1 package(s) [2024-11-24 09:46:25] INFO: Finished at 2024-11-24 09:46:25.018749, took: 0:00:00.517764 All cleanup done. Sun Nov 24 09:46:25 UTC 2024 - total duration: 0h 2m 12s. Sun Nov 24 09:46:25 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-fXriezKO, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2min 15.508s CPU time consumed: 8.467s