Running as unit: rb-build-amd64_12-70207.service; invocation ID: 8b7701d550c44f56bd40a8a32039187d ==================================================================================== Mon Sep 15 00:45:48 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_12) on jenkins, called using "ionos15-amd64 ionos1-amd64" as arguments. Mon Sep 15 00:45:48 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-tqgbrs08" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Sep 15 00:45:48 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Mon Sep 15 00:45:48 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-BfzvQ9' Mon Sep 15 00:45:48 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Mon Sep 15 00:45:48 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-apfP25' 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 ionos15-amd64.debian.net. 2nd build will be done on ionos1-amd64.debian.net. ============================================================================= Mon Sep 15 00:46:08 UTC 2025 I: starting to build readseq/unstable/amd64 on jenkins on '2025-09-15 00:45' Mon Sep 15 00:46:08 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_12/70207/console.log 1757897168 amd64 unstable readseq Mon Sep 15 00:46:08 UTC 2025 I: Downloading source for unstable/readseq=1-15 --2025-09-15 00:46:08-- 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% 208M=0s 2025-09-15 00:46:08 (208 MB/s) - ‘readseq_1-15.dsc’ saved [2069/2069] --2025-09-15 00:46:08-- 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% 208M=0s 2025-09-15 00:46:08 (208 MB/s) - ‘readseq_1-15.dsc’ saved [2069/2069] Mon Sep 15 00:46:08 UTC 2025 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----- Mon Sep 15 00:46:08 UTC 2025 I: Checking whether the package is not for us Mon Sep 15 00:46:08 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Mon Sep 15 00:46:08 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Mon Sep 15 00:46:08 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Mon Sep 15 00:46:08 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-UKJBHn' ==================================================================================== Sun Oct 18 07:09:08 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 readseq unstable /srv/reproducible-results/rbuild-debian/r-b-build.sI6ymfVk 1-15" as arguments. Sun Oct 18 07:09:08 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-RkfvB89D" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Oct 18 07:09:08 UTC 2026 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 (5922 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 (5922 kB/s) Download complete and in download only mode ============================================================================= Building readseq in unstable on amd64 on ionos15-amd64 now. Date: Sun Oct 18 07:09:08 UTC 2026 Date UTC: Sun Oct 18 07:09:08 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Oct 17 19:09:08 -12 2026 I: pbuilder-time-stamp: 1792307348 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 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/3243973/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=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c684e753be1045ce8d511da271240605' 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='3243973' 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.sI6ymfVk/pbuilderrc_R6N7 --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.sI6ymfVk/b1 --logfile b1/build.log readseq_1-15.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3243973/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 ... 19917 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} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libidn2-0{a} libmagic-mgc{a} libmagic1t64{a} libncbi6-dev{a} libncbi6t64{a} libp11-kit0{a} libpipeline1{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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, 37 newly installed, 0 to remove and 0 not upgraded. Need to get 26.5 MB of archives. After unpacking 116 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 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 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 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 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 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 13.26 [939 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libncbi6t64 amd64 6.1.20170106+dfsg2-6 [4107 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libncbi6-dev amd64 6.1.20170106+dfsg2-6 [5542 kB] Fetched 26.5 MB in 0s (148 MB/s) Preconfiguring packages ... 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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... 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_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. 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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 -j42 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 -j42 "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 'addseq': ureadseq.c:168:40: error: too many arguments to function 'V->isseqcharfirst8'; expected 0, have 1 168 | if (!(V->isseqcharfirst8) (*s)) continue; | ~~^~~~~~~~~~~~~~~~~~ ~~ ureadseq.c:108:9: note: declared here 108 | int (*isseqcharfirst8)(); /* Patch by o. strunk (ARB) to allow numbers in genbank sequences*/ | ^~~~~~~~~~~~~~~ ureadseq.c:170:40: error: too many arguments to function 'V->isseqchar'; expected 0, have 1 170 | if (!(V->isseqchar) (*s)) continue; | ~~^~~~~~~~~~~~ ~~ ureadseq.c:110:9: note: declared here 110 | int (*isseqchar)(); | ^~~~~~~~~ ureadseq.c: In function 'countseq': ureadseq.c:198:11: error: too many arguments to function 'V->isseqchar'; expected 0, have 1 198 | if ((V->isseqchar)(*s)) { | ~~^~~~~~~~~~~~ ~~ ureadseq.c:110:9: note: declared here 110 | int (*isseqchar)(); | ^~~~~~~~~ ureadseq.c: In function 'addinfo': ureadseq.c:217:16: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 217 | V->isseqchar = isAnyChar; | ^ ureadseq.c:127:5: note: 'isAnyChar' declared here 127 | int isAnyChar(int c) | ^~~~~~~~~ ureadseq.c:220:16: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 220 | V->isseqchar = isSeqChar; | ^ ureadseq.c:116:5: note: 'isSeqChar' declared here 116 | int isSeqChar(int c) | ^~~~~~~~~ ureadseq.c: In function 'readGenBank': ureadseq.c:351:22: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 351 | V->isseqchar = isSeqNumChar; | ^ ureadseq.c:121:5: note: 'isSeqNumChar' declared here 121 | int isSeqNumChar(int c) | ^~~~~~~~~~~~ ureadseq.c:352:28: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 352 | V->isseqcharfirst8 = isSeqChar; | ^ ureadseq.c:116:5: note: 'isSeqChar' declared here 116 | int isSeqChar(int c) | ^~~~~~~~~ ureadseq.c:368:21: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 368 | V->isseqchar = isSeqChar; | ^ ureadseq.c:116:5: note: 'isSeqChar' declared here 116 | int isSeqChar(int c) | ^~~~~~~~~ ureadseq.c: In function 'readSeqFp': ureadseq.c:1155:15: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 1155 | V.isseqchar = isSeqChar; | ^ ureadseq.c:116:5: note: 'isSeqChar' declared here 116 | int isSeqChar(int c) | ^~~~~~~~~ ureadseq.c: In function 'readSeq': ureadseq.c:1201:15: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 1201 | V.isseqchar = isSeqChar; | ^ ureadseq.c:116:5: note: 'isSeqChar' declared here 116 | int isSeqChar(int c) | ^~~~~~~~~ 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 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) | ^~~~~ make[1]: *** [Makefile:51: build] Error 1 make[1]: Leaving directory '/build/reproducible-path/readseq-1' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:8: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/3243973 and its subdirectories Starting cleanup. All cleanup done. Sun Oct 18 07:09:45 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-RkfvB89D, removing. /srv/reproducible-results/rbuild-debian/r-b-build.sI6ymfVk: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 15 00:46 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 15 00:46 b2 -rw------- 1 jenkins jenkins 3156 Sep 15 00:46 rbuildlog.xAMTLJo -rw-rw-r-- 1 jenkins jenkins 2069 Mar 14 2024 readseq_1-15.dsc /srv/reproducible-results/rbuild-debian/r-b-build.sI6ymfVk/b1: total 52 -rw-r--r-- 1 jenkins jenkins 51036 Sep 15 00:46 build.log /srv/reproducible-results/rbuild-debian/r-b-build.sI6ymfVk/b2: total 0 Mon Sep 15 00:46:47 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Oct 17 19:09:08 -12 2026 I: pbuilder-time-stamp: 1792307348 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 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/3243973/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=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c684e753be1045ce8d511da271240605' 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='3243973' 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.sI6ymfVk/pbuilderrc_R6N7 --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.sI6ymfVk/b1 --logfile b1/build.log readseq_1-15.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3243973/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 ... 19917 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} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libidn2-0{a} libmagic-mgc{a} libmagic1t64{a} libncbi6-dev{a} libncbi6t64{a} libp11-kit0{a} libpipeline1{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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, 37 newly installed, 0 to remove and 0 not upgraded. Need to get 26.5 MB of archives. After unpacking 116 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 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 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 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 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 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 13.26 [939 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 ncbi-data all 6.1.20170106+dfsg2-6 [3541 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libncbi6t64 amd64 6.1.20170106+dfsg2-6 [4107 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libncbi6-dev amd64 6.1.20170106+dfsg2-6 [5542 kB] Fetched 26.5 MB in 0s (148 MB/s) Preconfiguring packages ... 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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... 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_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. 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Unpacking libgnutls30t64:amd64 (3.8.10-2) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../34-ncbi-data_6.1.20170106+dfsg2-6_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg2-6) ... Selecting previously unselected package libncbi6t64:amd64. Preparing to unpack .../35-libncbi6t64_6.1.20170106+dfsg2-6_amd64.deb ... Unpacking libncbi6t64:amd64 (6.1.20170106+dfsg2-6) ... Selecting previously unselected package libncbi6-dev:amd64. Preparing to unpack .../36-libncbi6-dev_6.1.20170106+dfsg2-6_amd64.deb ... Unpacking libncbi6-dev:amd64 (6.1.20170106+dfsg2-6) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up ncbi-data (6.1.20170106+dfsg2-6) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... 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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 -j42 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 -j42 "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 'addseq': ureadseq.c:168:40: error: too many arguments to function 'V->isseqcharfirst8'; expected 0, have 1 168 | if (!(V->isseqcharfirst8) (*s)) continue; | ~~^~~~~~~~~~~~~~~~~~ ~~ ureadseq.c:108:9: note: declared here 108 | int (*isseqcharfirst8)(); /* Patch by o. strunk (ARB) to allow numbers in genbank sequences*/ | ^~~~~~~~~~~~~~~ ureadseq.c:170:40: error: too many arguments to function 'V->isseqchar'; expected 0, have 1 170 | if (!(V->isseqchar) (*s)) continue; | ~~^~~~~~~~~~~~ ~~ ureadseq.c:110:9: note: declared here 110 | int (*isseqchar)(); | ^~~~~~~~~ ureadseq.c: In function 'countseq': ureadseq.c:198:11: error: too many arguments to function 'V->isseqchar'; expected 0, have 1 198 | if ((V->isseqchar)(*s)) { | ~~^~~~~~~~~~~~ ~~ ureadseq.c:110:9: note: declared here 110 | int (*isseqchar)(); | ^~~~~~~~~ ureadseq.c: In function 'addinfo': ureadseq.c:217:16: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 217 | V->isseqchar = isAnyChar; | ^ ureadseq.c:127:5: note: 'isAnyChar' declared here 127 | int isAnyChar(int c) | ^~~~~~~~~ ureadseq.c:220:16: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 220 | V->isseqchar = isSeqChar; | ^ ureadseq.c:116:5: note: 'isSeqChar' declared here 116 | int isSeqChar(int c) | ^~~~~~~~~ ureadseq.c: In function 'readGenBank': ureadseq.c:351:22: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 351 | V->isseqchar = isSeqNumChar; | ^ ureadseq.c:121:5: note: 'isSeqNumChar' declared here 121 | int isSeqNumChar(int c) | ^~~~~~~~~~~~ ureadseq.c:352:28: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 352 | V->isseqcharfirst8 = isSeqChar; | ^ ureadseq.c:116:5: note: 'isSeqChar' declared here 116 | int isSeqChar(int c) | ^~~~~~~~~ ureadseq.c:368:21: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 368 | V->isseqchar = isSeqChar; | ^ ureadseq.c:116:5: note: 'isSeqChar' declared here 116 | int isSeqChar(int c) | ^~~~~~~~~ ureadseq.c: In function 'readSeqFp': ureadseq.c:1155:15: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 1155 | V.isseqchar = isSeqChar; | ^ ureadseq.c:116:5: note: 'isSeqChar' declared here 116 | int isSeqChar(int c) | ^~~~~~~~~ ureadseq.c: In function 'readSeq': ureadseq.c:1201:15: error: assignment to 'int (*)(void)' from incompatible pointer type 'int (*)(int)' [-Wincompatible-pointer-types] 1201 | V.isseqchar = isSeqChar; | ^ ureadseq.c:116:5: note: 'isSeqChar' declared here 116 | int isSeqChar(int c) | ^~~~~~~~~ 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 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) | ^~~~~ make[1]: *** [Makefile:51: build] Error 1 make[1]: Leaving directory '/build/reproducible-path/readseq-1' dh_auto_build: error: make -j42 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:8: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/3243973 and its subdirectories readseq failed to build from source. 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' Mon Sep 15 00:46:47 UTC 2025 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 83.4% -- replaced with stdout INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-15 00:46:48] INFO: Starting at 2025-09-15 00:46:48.014671 [2025-09-15 00:46:48] INFO: Generating the pages of 1 package(s) [2025-09-15 00:46:48] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/readseq didn't produce a buildlog, even though it has been built. [2025-09-15 00:46:48] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/readseq didn't produce a buildlog, even though it has been built. [2025-09-15 00:46:48] INFO: Finished at 2025-09-15 00:46:48.280616, took: 0:00:00.265948 Mon Sep 15 00:46:48 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/readseq.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/readseq_1-15.rbuild.log: 81.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/readseq_1-15.rbuild.log.gz [2025-09-15 00:46:48] INFO: Starting at 2025-09-15 00:46:48.597513 [2025-09-15 00:46:48] INFO: Generating the pages of 1 package(s) [2025-09-15 00:46:48] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/readseq_1-15.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/readseq_1-15.diff.gz is missing [2025-09-15 00:46:48] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/readseq didn't produce a buildlog, even though it has been built. [2025-09-15 00:46:48] INFO: Finished at 2025-09-15 00:46:48.866804, took: 0:00:00.269295 All cleanup done. Mon Sep 15 00:46:48 UTC 2025 - total duration: 0h 0m 59s. Mon Sep 15 00:46:48 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-tqgbrs08, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 1min 956ms CPU time consumed: 2.462s Memory peak: 39M (swap: 0B)