Running as unit: rb-build-amd64_28-73040.service; invocation ID: 4fa5ddc5b97e4e06ae3cdc0097500c51 ==================================================================================== Thu Sep 18 19:23:47 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_28) on jenkins, called using "ionos15-amd64 ionos11-amd64" as arguments. Thu Sep 18 19:23:47 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-yUrAovFI" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 19:23:47 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Sep 18 19:23:47 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-6oNzuW' Thu Sep 18 19:23:47 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Sep 18 19:23:47 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-nYwkbd' ok, let's check if repeatmasker-recon is building anywhere yet… ok, repeatmasker-recon is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of repeatmasker-recon in unstable on amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos11-amd64.debian.net. ============================================================================= Thu Sep 18 19:24:00 UTC 2025 I: starting to build repeatmasker-recon/unstable/amd64 on jenkins on '2025-09-18 19:23' Thu Sep 18 19:24:00 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_28/73040/console.log 1758223440 amd64 unstable repeatmasker-recon Thu Sep 18 19:24:00 UTC 2025 I: Downloading source for unstable/repeatmasker-recon=1.08-8 --2025-09-18 19:24:00-- http://deb.debian.org/debian/pool/main/r/repeatmasker-recon/repeatmasker-recon_1.08-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2070 (2.0K) [text/prs.lines.tag] Saving to: ‘repeatmasker-recon_1.08-8.dsc’ 0K .. 100% 9.13M=0s 2025-09-18 19:24:00 (9.13 MB/s) - ‘repeatmasker-recon_1.08-8.dsc’ saved [2070/2070] --2025-09-18 19:24:00-- http://deb.debian.org/debian/pool/main/r/repeatmasker-recon/repeatmasker-recon_1.08-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2070 (2.0K) [text/prs.lines.tag] Saving to: ‘repeatmasker-recon_1.08-8.dsc’ 0K .. 100% 9.13M=0s 2025-09-18 19:24:00 (9.13 MB/s) - ‘repeatmasker-recon_1.08-8.dsc’ saved [2070/2070] Thu Sep 18 19:24:00 UTC 2025 I: repeatmasker-recon_1.08-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: repeatmasker-recon Binary: repeatmasker-recon Architecture: any Version: 1.08-8 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Andreas Tille , Homepage: https://www.repeatmasker.org/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/repeatmasker-recon Vcs-Git: https://salsa.debian.org/med-team/repeatmasker-recon.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: repeatmasker-recon deb science optional arch=any Checksums-Sha1: a91b9f54dc277248c6848c2584531f7538bec3b4 108477 repeatmasker-recon_1.08.orig.tar.gz 7742af75fe931bb48fed7f73097141e28ec8d5c4 5980 repeatmasker-recon_1.08-8.debian.tar.xz Checksums-Sha256: 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 108477 repeatmasker-recon_1.08.orig.tar.gz 4d1ac5ddbc014ba414efad01003c4df7fcb6046debba1f75376aca2123be36b6 5980 repeatmasker-recon_1.08-8.debian.tar.xz Files: 48c5c650a312bc1cc3fdddcfd943deb0 108477 repeatmasker-recon_1.08.orig.tar.gz 1835d963ebdb4632412a087475e79aa5 5980 repeatmasker-recon_1.08-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmXxv+oACgkQPCZ2P2xn 5uK6Uw//YuwYNshpmxC7WNweGtXXYB2aC+D9cdEn0mxwg8iXhpNHdnA0e+NzpDSe +HHjf73zzbwYjibS/tMcU5+PKCRrwuReRw9A0b9+iSxtCzL/hFoTgivzLnPK6Lkg 9tUOUHWH+m3uw1/2qnpaMA8sfaEBynKFNZPv6vDXlXTs5a66zSj9biUM+8CGqae9 sUH+VHwln3vmiBRS6/UtIsXIl82KkXms3ql/jOgH+J06+wqIfBjQ/tkwqgup+V9v 9e3VdLqzLISXdqJflX8OsdnsU4SPLHyd1ju5GC/y8WLK3KIU1OsQX6O6+G9LYfAU RXjaSADmFd4WJk5V7OnfOhcbUA+skq0EbmFI2FaFe2WDxwUPlMH3qJ2SnwNqJL6f CmIrLPp+vs8vxLmf8zbeQ98I2/K1Ln3gKzEs2Vb6LRGeo5/bjllUUdXxlU8THxEi jtoNyEeCiOU8Ko3RRvRjxiD1M9kiT99eIoQbFwmukcxvUoor4XrQ0KVxUYvga3et xF6EydndzXKZGSTspk/iFezuBAsH6ukoBqyd1PcLBc7lz1byAa5bAAs8Ijb/k5/b w5+13tiLK1mXcTPinSRnTLEzR5zpfbuETeNbDhiYZW5pwA6aj2N+1/uuk4lr3i5u kyBCl4CkeRiLrIG9ZnHdaCQcdMLjsDGITyq4ZOF+SEnlO27Pp7I= =u+mC -----END PGP SIGNATURE----- Thu Sep 18 19:24:00 UTC 2025 I: Checking whether the package is not for us Thu Sep 18 19:24:00 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu Sep 18 19:24:00 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu Sep 18 19:24:00 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Sep 18 19:24:00 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-PTaQJa' ==================================================================================== Thu Oct 22 01:47:00 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 repeatmasker-recon unstable /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu 1.08-8" as arguments. Thu Oct 22 01:47:00 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-SEJGRz1y" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Oct 22 01:47:00 UTC 2026 I: Downloading source for unstable/repeatmasker-recon=1.08-8 Reading package lists... NOTICE: 'repeatmasker-recon' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/repeatmasker-recon.git Please use: git clone https://salsa.debian.org/med-team/repeatmasker-recon.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 117 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (dsc) [2070 B] Get:2 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (tar) [108 kB] Get:3 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (diff) [5980 B] Fetched 117 kB in 0s (1018 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'repeatmasker-recon' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/repeatmasker-recon.git Please use: git clone https://salsa.debian.org/med-team/repeatmasker-recon.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 117 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (dsc) [2070 B] Get:2 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (tar) [108 kB] Get:3 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (diff) [5980 B] Fetched 117 kB in 0s (1018 kB/s) Download complete and in download only mode ============================================================================= Building repeatmasker-recon in unstable on amd64 on ionos15-amd64 now. Date: Thu Oct 22 01:47:01 UTC 2026 Date UTC: Thu Oct 22 01:47:01 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: Wed Oct 21 13:47:01 -12 2026 I: pbuilder-time-stamp: 1792633621 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 [repeatmasker-recon_1.08-8.dsc] I: copying [./repeatmasker-recon_1.08.orig.tar.gz] I: copying [./repeatmasker-recon_1.08-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./repeatmasker-recon_1.08-8.dsc: no acceptable signature found dpkg-source: info: extracting repeatmasker-recon in repeatmasker-recon-1.08 dpkg-source: info: unpacking repeatmasker-recon_1.08.orig.tar.gz dpkg-source: info: unpacking repeatmasker-recon_1.08-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-udpate-paths.patch dpkg-source: info: applying 0002-fix_binary_name.patch dpkg-source: info: applying 0003-hardening.patch dpkg-source: info: applying 0004-missing-include.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3731827/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='2e8ecbca3207465193781006b667c19c' 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='3731827' 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.BNxc6URu/pbuilderrc_4Zw6 --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.BNxc6URu/b1 --logfile b1/build.log repeatmasker-recon_1.08-8.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/3731827/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) 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. 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.2 MB of archives. After unpacking 42.7 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] Fetched 11.2 MB in 3s (3654 kB/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. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... 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_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Setting up libpipeline1:amd64 (1.5.8-1) ... 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) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/repeatmasker-recon-1.08/ && 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 > ../repeatmasker-recon_1.08-8_source.changes dpkg-buildpackage: info: source package repeatmasker-recon dpkg-buildpackage: info: source version 1.08-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j42 clean make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' rm -f imagespread eledef eleredef edgeredef famdef *.o *~ *.Addrs *.Counts *.pixie Makefile.bak core imagespread eledef eleredef edgeredef famdef TAGS make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' dh_autoreconf_clean -O--sourcedirectory=src debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' rm -rf bin dh_clean make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src cd src && make -j42 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro imagespread.c -o imagespread gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eledef.c -o eledef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eleredef.c -o eleredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro edgeredef.c -o edgeredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro famdef.c -o famdef In file included from ele.h:1, from famdef.c:1: msps.h: In function 'scan_msp': In file included from imagespread.c:2: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from ele.h:1, from edgeredef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from eledef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ele.h:1, from eleredef.c:5: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d eledef.c: In function 'main': eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | freopen(ele_name, "w", all_ele);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c:246:7: note: in expansion of macro 'DUMBBELL' 246 | DUMBBELL; | ^~~~~~~~ eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | freopen(ele_name, "w", all_ele);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c:253:5: note: in expansion of macro 'DUMBBELL' 253 | DUMBBELL; | ^~~~~~~~ edgeredef.c: In function 'general_edge_redef': edgeredef.c:200:5: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 200 | system(command); | ^~~~~~~~~~~~~~~ eleredef.c: In function 'main': eleredef.c:239:70: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] 239 | printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) ); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' echo "Do not run tests since there exists no testsuite.sh needed to run those in the package" Do not run tests since there exists no testsuite.sh needed to run those in the package make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules execute_before_dh_auto_install make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' mkdir -p bin make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' dh_auto_install --destdir=debian/repeatmasker-recon/ -O--sourcedirectory=src cd src && make -j42 install DESTDIR=/build/reproducible-path/repeatmasker-recon-1.08/debian/repeatmasker-recon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' cp imagespread eledef eleredef edgeredef famdef ../bin/ make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' dh_install -O--sourcedirectory=src debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' cp scripts/recon.pl debian/repeatmasker-recon/usr/bin/repeatmasker-recon cp scripts/MSPCollect.pl debian/repeatmasker-recon/usr/bin/MSPCollect make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'repeatmasker-recon' in '../repeatmasker-recon_1.08-8_amd64.deb'. dpkg-deb: building package 'repeatmasker-recon-dbgsym' in '../repeatmasker-recon-dbgsym_1.08-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../repeatmasker-recon_1.08-8_amd64.buildinfo dpkg-genchanges --build=binary -O../repeatmasker-recon_1.08-8_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/3731827 and its subdirectories I: Current time: Wed Oct 21 13:50:16 -12 2026 I: pbuilder-time-stamp: 1792633816 Thu Oct 22 01:50:16 UTC 2026 I: Signing ./b1/repeatmasker-recon_1.08-8_amd64.buildinfo as repeatmasker-recon_1.08-8_amd64.buildinfo.asc Thu Oct 22 01:50:16 UTC 2026 I: Signed ./b1/repeatmasker-recon_1.08-8_amd64.buildinfo as ./b1/repeatmasker-recon_1.08-8_amd64.buildinfo.asc Thu Oct 22 01:50:16 UTC 2026 - build #1 for repeatmasker-recon/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Thu Oct 22 01:50:16 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-SEJGRz1y, removing. /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 19:27 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 19:24 b2 -rw------- 1 jenkins jenkins 3245 Sep 18 19:24 rbuildlog.3dCOOBE -rw-rw-r-- 1 jenkins jenkins 2070 Mar 13 2024 repeatmasker-recon_1.08-8.dsc /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/b1: total 276 -rw-r--r-- 1 jenkins jenkins 44154 Sep 18 19:27 build.log -rw-r--r-- 1 jenkins jenkins 113224 Sep 18 19:27 repeatmasker-recon-dbgsym_1.08-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 5980 Sep 18 19:27 repeatmasker-recon_1.08-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2070 Sep 18 19:27 repeatmasker-recon_1.08-8.dsc -rw-r--r-- 1 jenkins jenkins 4941 Sep 18 19:27 repeatmasker-recon_1.08-8_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5823 Sep 18 19:27 repeatmasker-recon_1.08-8_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1545 Sep 18 19:27 repeatmasker-recon_1.08-8_amd64.changes -rw-r--r-- 1 jenkins jenkins 85216 Sep 18 19:27 repeatmasker-recon_1.08-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 1376 Sep 18 19:27 repeatmasker-recon_1.08-8_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/b2: total 0 Thu Sep 18 19:27:17 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Oct 21 13:47:01 -12 2026 I: pbuilder-time-stamp: 1792633621 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 [repeatmasker-recon_1.08-8.dsc] I: copying [./repeatmasker-recon_1.08.orig.tar.gz] I: copying [./repeatmasker-recon_1.08-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./repeatmasker-recon_1.08-8.dsc: no acceptable signature found dpkg-source: info: extracting repeatmasker-recon in repeatmasker-recon-1.08 dpkg-source: info: unpacking repeatmasker-recon_1.08.orig.tar.gz dpkg-source: info: unpacking repeatmasker-recon_1.08-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-udpate-paths.patch dpkg-source: info: applying 0002-fix_binary_name.patch dpkg-source: info: applying 0003-hardening.patch dpkg-source: info: applying 0004-missing-include.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3731827/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='2e8ecbca3207465193781006b667c19c' 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='3731827' 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.BNxc6URu/pbuilderrc_4Zw6 --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.BNxc6URu/b1 --logfile b1/build.log repeatmasker-recon_1.08-8.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/3731827/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) 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. 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.2 MB of archives. After unpacking 42.7 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] Fetched 11.2 MB in 3s (3654 kB/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. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... 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_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Setting up libpipeline1:amd64 (1.5.8-1) ... 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) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/repeatmasker-recon-1.08/ && 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 > ../repeatmasker-recon_1.08-8_source.changes dpkg-buildpackage: info: source package repeatmasker-recon dpkg-buildpackage: info: source version 1.08-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j42 clean make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' rm -f imagespread eledef eleredef edgeredef famdef *.o *~ *.Addrs *.Counts *.pixie Makefile.bak core imagespread eledef eleredef edgeredef famdef TAGS make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' dh_autoreconf_clean -O--sourcedirectory=src debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' rm -rf bin dh_clean make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src cd src && make -j42 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro imagespread.c -o imagespread gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eledef.c -o eledef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eleredef.c -o eleredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro edgeredef.c -o edgeredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro famdef.c -o famdef In file included from ele.h:1, from famdef.c:1: msps.h: In function 'scan_msp': In file included from imagespread.c:2: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from ele.h:1, from edgeredef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from eledef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ele.h:1, from eleredef.c:5: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d eledef.c: In function 'main': eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | freopen(ele_name, "w", all_ele);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c:246:7: note: in expansion of macro 'DUMBBELL' 246 | DUMBBELL; | ^~~~~~~~ eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | freopen(ele_name, "w", all_ele);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c:253:5: note: in expansion of macro 'DUMBBELL' 253 | DUMBBELL; | ^~~~~~~~ edgeredef.c: In function 'general_edge_redef': edgeredef.c:200:5: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 200 | system(command); | ^~~~~~~~~~~~~~~ eleredef.c: In function 'main': eleredef.c:239:70: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] 239 | printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) ); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' echo "Do not run tests since there exists no testsuite.sh needed to run those in the package" Do not run tests since there exists no testsuite.sh needed to run those in the package make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules execute_before_dh_auto_install make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' mkdir -p bin make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' dh_auto_install --destdir=debian/repeatmasker-recon/ -O--sourcedirectory=src cd src && make -j42 install DESTDIR=/build/reproducible-path/repeatmasker-recon-1.08/debian/repeatmasker-recon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' cp imagespread eledef eleredef edgeredef famdef ../bin/ make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' dh_install -O--sourcedirectory=src debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' cp scripts/recon.pl debian/repeatmasker-recon/usr/bin/repeatmasker-recon cp scripts/MSPCollect.pl debian/repeatmasker-recon/usr/bin/MSPCollect make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'repeatmasker-recon' in '../repeatmasker-recon_1.08-8_amd64.deb'. dpkg-deb: building package 'repeatmasker-recon-dbgsym' in '../repeatmasker-recon-dbgsym_1.08-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../repeatmasker-recon_1.08-8_amd64.buildinfo dpkg-genchanges --build=binary -O../repeatmasker-recon_1.08-8_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/3731827 and its subdirectories I: Current time: Wed Oct 21 13:50:16 -12 2026 I: pbuilder-time-stamp: 1792633816 Thu Sep 18 19:27:17 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Thu Sep 18 19:27:17 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Thu Sep 18 19:27:17 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Sep 18 19:27:17 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-UUyFZ6' ==================================================================================== Thu Sep 18 19:27:17 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "2 repeatmasker-recon unstable /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu 1.08-8" as arguments. Thu Sep 18 19:27:17 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-Vtnsv4lN" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Sep 18 19:27:17 UTC 2025 I: Downloading source for unstable/repeatmasker-recon=1.08-8 Reading package lists... NOTICE: 'repeatmasker-recon' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/repeatmasker-recon.git Please use: git clone https://salsa.debian.org/med-team/repeatmasker-recon.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 117 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (dsc) [2070 B] Get:2 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (tar) [108 kB] Get:3 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (diff) [5980 B] Fetched 117 kB in 0s (702 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'repeatmasker-recon' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/repeatmasker-recon.git Please use: git clone https://salsa.debian.org/med-team/repeatmasker-recon.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 117 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (dsc) [2070 B] Get:2 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (tar) [108 kB] Get:3 http://deb.debian.org/debian unstable/main repeatmasker-recon 1.08-8 (diff) [5980 B] Fetched 117 kB in 0s (702 kB/s) Download complete and in download only mode ============================================================================= Re-Building repeatmasker-recon in unstable on amd64 on ionos11-amd64 now. Date: Thu Sep 18 19:27:18 UTC 2025 Date UTC: Thu Sep 18 19:27:18 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/pbuilderrc_oDKc + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' repeatmasker-recon = debian-installer -o repeatmasker-recon = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' repeatmasker-recon = u-boot ']' + case "${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.BNxc6URu/pbuilderrc_oDKc --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.BNxc6URu/b2 --logfile b2/build.log repeatmasker-recon_1.08-8.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: Fri Sep 19 09:27:18 +14 2025 I: pbuilder-time-stamp: 1758223638 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 [repeatmasker-recon_1.08-8.dsc] I: copying [./repeatmasker-recon_1.08.orig.tar.gz] I: copying [./repeatmasker-recon_1.08-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./repeatmasker-recon_1.08-8.dsc: no acceptable signature found dpkg-source: info: extracting repeatmasker-recon in repeatmasker-recon-1.08 dpkg-source: info: unpacking repeatmasker-recon_1.08.orig.tar.gz dpkg-source: info: unpacking repeatmasker-recon_1.08-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-udpate-paths.patch dpkg-source: info: applying 0002-fix_binary_name.patch dpkg-source: info: applying 0003-hardening.patch dpkg-source: info: applying 0004-missing-include.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1584778/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-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 Sep 18 19:27 /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/1584778/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1584778/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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(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=40 ' 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=4a924c1f43c9419c89a993a3c9ec1b42 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=1584778 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.BNxc6URu/pbuilderrc_oDKc --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.BNxc6URu/b2 --logfile b2/build.log repeatmasker-recon_1.08-8.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+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 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1584778/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) 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. 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} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.2 MB of archives. After unpacking 42.7 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] Fetched 11.2 MB in 0s (34.1 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. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... 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_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1584778/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1584778/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/repeatmasker-recon-1.08/ && 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 > ../repeatmasker-recon_1.08-8_source.changes dpkg-buildpackage: info: source package repeatmasker-recon dpkg-buildpackage: info: source version 1.08-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j40 clean make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' rm -f imagespread eledef eleredef edgeredef famdef *.o *~ *.Addrs *.Counts *.pixie Makefile.bak core imagespread eledef eleredef edgeredef famdef TAGS make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' dh_autoreconf_clean -O--sourcedirectory=src debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' rm -rf bin dh_clean make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src cd src && make -j40 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro imagespread.c -o imagespread gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eledef.c -o eledef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eleredef.c -o eleredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro edgeredef.c -o edgeredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro famdef.c -o famdef In file included from eledef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c: In function 'main': eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | freopen(ele_name, "w", all_ele);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c:246:7: note: in expansion of macro 'DUMBBELL' 246 | DUMBBELL; | ^~~~~~~~ eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] 95 | freopen(ele_name, "w", all_ele);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c:253:5: note: in expansion of macro 'DUMBBELL' 253 | DUMBBELL; | ^~~~~~~~ In file included from imagespread.c:2: msps.h: In function 'scan_msp': In file included from ele.h:1, from eleredef.c:5: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ele.h:1, from edgeredef.c:1: msps.h: In function 'scan_msp': In file included from ele.h:1, from famdef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d eleredef.c: In function 'main': eleredef.c:239:70: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] 239 | printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) ); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from msps.h:4: seqlist.h: In function 'GetSeqNames': seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ edgeredef.c: In function 'general_edge_redef': edgeredef.c:200:5: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 200 | system(command); | ^~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' echo "Do not run tests since there exists no testsuite.sh needed to run those in the package" Do not run tests since there exists no testsuite.sh needed to run those in the package make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules execute_before_dh_auto_install make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' mkdir -p bin make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' dh_auto_install --destdir=debian/repeatmasker-recon/ -O--sourcedirectory=src cd src && make -j40 install DESTDIR=/build/reproducible-path/repeatmasker-recon-1.08/debian/repeatmasker-recon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' cp imagespread eledef eleredef edgeredef famdef ../bin/ make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' dh_install -O--sourcedirectory=src debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' cp scripts/recon.pl debian/repeatmasker-recon/usr/bin/repeatmasker-recon cp scripts/MSPCollect.pl debian/repeatmasker-recon/usr/bin/MSPCollect make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'repeatmasker-recon-dbgsym' in '../repeatmasker-recon-dbgsym_1.08-8_amd64.deb'. dpkg-deb: building package 'repeatmasker-recon' in '../repeatmasker-recon_1.08-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../repeatmasker-recon_1.08-8_amd64.buildinfo dpkg-genchanges --build=binary -O../repeatmasker-recon_1.08-8_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/1584778/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1584778/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/1584778 and its subdirectories I: Current time: Fri Sep 19 09:28:48 +14 2025 I: pbuilder-time-stamp: 1758223728 + false + set +x Thu Sep 18 19:28:48 UTC 2025 I: Signing ./b2/repeatmasker-recon_1.08-8_amd64.buildinfo as repeatmasker-recon_1.08-8_amd64.buildinfo.asc Thu Sep 18 19:28:48 UTC 2025 I: Signed ./b2/repeatmasker-recon_1.08-8_amd64.buildinfo as ./b2/repeatmasker-recon_1.08-8_amd64.buildinfo.asc Thu Sep 18 19:28:48 UTC 2025 - build #2 for repeatmasker-recon/unstable/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Thu Sep 18 19:28:48 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Vtnsv4lN, removing. /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu: total 60 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 19:27 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 18 19:28 b2 -rw------- 1 jenkins jenkins 47688 Sep 18 19:27 rbuildlog.3dCOOBE -rw-rw-r-- 1 jenkins jenkins 2070 Mar 13 2024 repeatmasker-recon_1.08-8.dsc /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/b1: total 284 -rw-r--r-- 1 jenkins jenkins 44154 Sep 18 19:27 build.log -rw-r--r-- 1 jenkins jenkins 113224 Sep 18 19:27 repeatmasker-recon-dbgsym_1.08-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 5980 Sep 18 19:27 repeatmasker-recon_1.08-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2070 Sep 18 19:27 repeatmasker-recon_1.08-8.dsc -rw-r--r-- 1 jenkins jenkins 4941 Sep 18 19:27 repeatmasker-recon_1.08-8_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5823 Sep 18 19:27 repeatmasker-recon_1.08-8_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1545 Sep 18 19:27 repeatmasker-recon_1.08-8_amd64.changes -rw-r--r-- 1 jenkins jenkins 85216 Sep 18 19:27 repeatmasker-recon_1.08-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 1376 Sep 18 19:27 repeatmasker-recon_1.08-8_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/b2: total 280 -rw-rw-r-- 1 jenkins jenkins 46080 Sep 18 19:28 build.log -rw-r--r-- 1 jenkins jenkins 113224 Sep 18 19:28 repeatmasker-recon-dbgsym_1.08-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 5980 Sep 18 19:28 repeatmasker-recon_1.08-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2070 Sep 18 19:28 repeatmasker-recon_1.08-8.dsc -rw-rw-r-- 1 jenkins jenkins 4941 Sep 18 19:28 repeatmasker-recon_1.08-8_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5823 Sep 18 19:28 repeatmasker-recon_1.08-8_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1545 Sep 18 19:28 repeatmasker-recon_1.08-8_amd64.changes -rw-r--r-- 1 jenkins jenkins 85216 Sep 18 19:28 repeatmasker-recon_1.08-8_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1376 Sep 18 19:28 repeatmasker-recon_1.08-8_source.changes Thu Sep 18 19:28:49 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Thu Sep 18 19:28:49 UTC 2025 I: repeatmasker-recon_1.08-8_amd64.changes: Format: 1.8 Date: Wed, 13 Mar 2024 16:00:34 +0100 Source: repeatmasker-recon Binary: repeatmasker-recon repeatmasker-recon-dbgsym Architecture: amd64 Version: 1.08-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: repeatmasker-recon - finds repeat families from biological sequences Changes: repeatmasker-recon (1.08-8) unstable; urgency=medium . * Team upload. * Add patch to add in missing include. Close: #1066541 * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 08c0617e9411ace32ce5cc29262f7cec7b9bfa7b 113224 repeatmasker-recon-dbgsym_1.08-8_amd64.deb 64c0bf8564832e4cdc3f474ddcbe62533f633b41 4941 repeatmasker-recon_1.08-8_amd64.buildinfo f8dbc534a4688154b168878a2b5ac64192398ede 85216 repeatmasker-recon_1.08-8_amd64.deb Checksums-Sha256: 2d41365471d0a9203adb9299c39c64f701698d3cab3b94e2b96bbb381d8c25b0 113224 repeatmasker-recon-dbgsym_1.08-8_amd64.deb b1bb49a6441aef4ce8418ae6b3f3868bc6ef4f46b59fd147d182d2d20401142b 4941 repeatmasker-recon_1.08-8_amd64.buildinfo 3f260d203178fecafef530e0e05505c7fd5840a45489c99b01deed7703d691ad 85216 repeatmasker-recon_1.08-8_amd64.deb Files: e4958994a7f315fd5df2fdc2726ea4fd 113224 debug optional repeatmasker-recon-dbgsym_1.08-8_amd64.deb ee5ac0eb15b351b888f4c8e611100c97 4941 science optional repeatmasker-recon_1.08-8_amd64.buildinfo 0111149cfcdd2f9c8d082b55d274d04c 85216 science optional repeatmasker-recon_1.08-8_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/repeatmasker-recon_1.08-8.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/repeatmasker-recon_1.08-8.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/repeatmasker-recon_1.08-8.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/repeatmasker-recon_1.08-8.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/repeatmasker-recon_1.08-8_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/repeatmasker-recon_1.08-8.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-18 19:27:17.014940721 +0000 +++ b2/build.log 2025-09-18 19:28:49.323071394 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Oct 21 13:47:01 -12 2026 -I: pbuilder-time-stamp: 1792633621 +I: Current time: Fri Sep 19 09:27:18 +14 2025 +I: pbuilder-time-stamp: 1758223638 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ dpkg-source: info: applying 0004-missing-include.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3731827/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1584778/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Sep 18 19:27 /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/1584778/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1584778/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' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=40 ' + 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='2e8ecbca3207465193781006b667c19c' - 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='3731827' - PS1='# ' - PS2='> ' + INVOCATION_ID=4a924c1f43c9419c89a993a3c9ec1b42 + 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=1584778 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.BNxc6URu/pbuilderrc_4Zw6 --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.BNxc6URu/b1 --logfile b1/build.log repeatmasker-recon_1.08-8.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' + 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.BNxc6URu/pbuilderrc_oDKc --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.BNxc6URu/b2 --logfile b2/build.log repeatmasker-recon_1.08-8.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 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/3731827/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1584778/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -138,7 +170,7 @@ 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] -Fetched 11.2 MB in 3s (3654 kB/s) +Fetched 11.2 MB in 0s (34.1 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.) @@ -269,7 +301,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/repeatmasker-recon-1.08/ && 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 > ../repeatmasker-recon_1.08-8_source.changes +I: user script /srv/workspace/pbuilder/1584778/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1584778/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/repeatmasker-recon-1.08/ && 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 > ../repeatmasker-recon_1.08-8_source.changes dpkg-buildpackage: info: source package repeatmasker-recon dpkg-buildpackage: info: source version 1.08-8 dpkg-buildpackage: info: source distribution unstable @@ -279,7 +315,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j42 clean + cd src && make -j40 clean make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' rm -f imagespread eledef eleredef edgeredef famdef *.o *~ *.Addrs *.Counts *.pixie Makefile.bak core imagespread eledef eleredef edgeredef famdef TAGS make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' @@ -295,17 +331,14 @@ dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src - cd src && make -j42 "INSTALL=install --strip-program=true" + cd src && make -j40 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro imagespread.c -o imagespread gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eledef.c -o eledef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eleredef.c -o eleredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro edgeredef.c -o edgeredef gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/repeatmasker-recon-1.08=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro famdef.c -o famdef -In file included from ele.h:1, - from famdef.c:1: -msps.h: In function 'scan_msp': -In file included from imagespread.c:2: +In file included from eledef.c:1: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { @@ -313,48 +346,18 @@ | | | | long int * int32_t * {aka int *} | %d -msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] - 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { - | ~~^ ~~~~~~~~~~~ - | | | - | long int * int32_t * {aka int *} - | %d msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d -msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] - 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { - | ~~^ ~~~~~~~~~~~~~~~~~~~ - | | | - | long int * int32_t * {aka int *} - | %d -msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] - 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { - | ~~^ ~~~~~~~~~~~~~~~~~~~ - | | | - | long int * int32_t * {aka int *} - | %d -msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] - 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { - | ~~^ ~~~~~~~~~~~~~~~~~~~ - | | | - | long int * int32_t * {aka int *} - | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d -msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] - 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { - | ~~^ ~~~~~~~~~~~~~~~~~~~ - | | | - | long int * int32_t * {aka int *} - | %d msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ @@ -367,8 +370,28 @@ | | | | long int * int32_t * {aka int *} | %d +In file included from msps.h:4: +seqlist.h: In function 'GetSeqNames': +seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 19 | fgets(line, 255, seq_list); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +eledef.c: In function 'main': +eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] + 95 | freopen(ele_name, "w", all_ele);\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +eledef.c:246:7: note: in expansion of macro 'DUMBBELL' + 246 | DUMBBELL; + | ^~~~~~~~ +eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] + 95 | freopen(ele_name, "w", all_ele);\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +eledef.c:253:5: note: in expansion of macro 'DUMBBELL' + 253 | DUMBBELL; + | ^~~~~~~~ +In file included from imagespread.c:2: +msps.h: In function 'scan_msp': In file included from ele.h:1, - from edgeredef.c:1: + from eleredef.c:5: msps.h: In function 'scan_msp': msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { @@ -382,6 +405,18 @@ | | | | long int * int32_t * {aka int *} | %d +msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] + 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { + | ~~^ ~~~~~~~~~~~ + | | | + | long int * int32_t * {aka int *} + | %d +msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] + 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { + | ~~^ ~~~~~~~~~~~~~~~~~~~ + | | | + | long int * int32_t * {aka int *} + | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ @@ -400,25 +435,6 @@ | | | | long int * int32_t * {aka int *} | %d -In file included from msps.h:4: -seqlist.h: In function 'GetSeqNames': -seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 19 | fgets(line, 255, seq_list); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from eledef.c:1: -msps.h: In function 'scan_msp': -msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] - 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { - | ~~^ ~~~~~~~~~~~ - | | | - | long int * int32_t * {aka int *} - | %d -msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] - 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { - | ~~^ ~~~~~~~~~~~~~~~~~~~ - | | | - | long int * int32_t * {aka int *} - | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ @@ -442,19 +458,18 @@ seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from msps.h:4: -seqlist.h: In function 'GetSeqNames': -In file included from msps.h:4: -seqlist.h: In function 'GetSeqNames': -seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 19 | fgets(line, 255, seq_list); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 19 | fgets(line, 255, seq_list); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ele.h:1, - from eleredef.c:5: + from edgeredef.c:1: msps.h: In function 'scan_msp': +In file included from ele.h:1, + from famdef.c:1: +msps.h: In function 'scan_msp': +msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] + 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { + | ~~^ ~~~~~~~~~~~ + | | | + | long int * int32_t * {aka int *} + | %d msps.h:116:25: warning: format '%ld' expects argument of type 'long int *', but argument 3 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ @@ -467,6 +482,18 @@ | | | | long int * int32_t * {aka int *} | %d +msps.h:116:32: warning: format '%ld' expects argument of type 'long int *', but argument 5 has type 'int32_t *' {aka 'int *'} [-Wformat=] + 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { + | ~~^ ~~~~~~~~~~~~~~~~~~~ + | | | + | long int * int32_t * {aka int *} + | %d +msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] + 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { + | ~~^ ~~~~~~~~~~~~~~~~~~~ + | | | + | long int * int32_t * {aka int *} + | %d msps.h:116:36: warning: format '%ld' expects argument of type 'long int *', but argument 6 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ @@ -479,29 +506,24 @@ | | | | long int * int32_t * {aka int *} | %d +msps.h:116:43: warning: format '%ld' expects argument of type 'long int *', but argument 8 has type 'int32_t *' {aka 'int *'} [-Wformat=] + 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { + | ~~^ ~~~~~~~~~~~~~~~~~~~ + | | | + | long int * int32_t * {aka int *} + | %d +msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] + 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { + | ~~^ ~~~~~~~~~~~~~~~~~~~ + | | | + | long int * int32_t * {aka int *} + | %d msps.h:116:47: warning: format '%ld' expects argument of type 'long int *', but argument 9 has type 'int32_t *' {aka 'int *'} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d -eledef.c: In function 'main': -eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] - 95 | freopen(ele_name, "w", all_ele);\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -eledef.c:246:7: note: in expansion of macro 'DUMBBELL' - 246 | DUMBBELL; - | ^~~~~~~~ -eledef.c:95:13: warning: ignoring return value of 'freopen' declared with attribute 'warn_unused_result' [-Wunused-result] - 95 | freopen(ele_name, "w", all_ele);\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -eledef.c:253:5: note: in expansion of macro 'DUMBBELL' - 253 | DUMBBELL; - | ^~~~~~~~ -edgeredef.c: In function 'general_edge_redef': -edgeredef.c:200:5: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 200 | system(command); - | ^~~~~~~~~~~~~~~ eleredef.c: In function 'main': eleredef.c:239:70: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=] 239 | printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) ); @@ -514,6 +536,20 @@ seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from msps.h:4: +seqlist.h: In function 'GetSeqNames': +seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 19 | fgets(line, 255, seq_list); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from msps.h:4: +seqlist.h: In function 'GetSeqNames': +seqlist.h:19:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 19 | fgets(line, 255, seq_list); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +edgeredef.c: In function 'general_edge_redef': +edgeredef.c:200:5: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 200 | system(command); + | ^~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08' @@ -528,7 +564,7 @@ mkdir -p bin make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08' dh_auto_install --destdir=debian/repeatmasker-recon/ -O--sourcedirectory=src - cd src && make -j42 install DESTDIR=/build/reproducible-path/repeatmasker-recon-1.08/debian/repeatmasker-recon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd src && make -j40 install DESTDIR=/build/reproducible-path/repeatmasker-recon-1.08/debian/repeatmasker-recon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/repeatmasker-recon-1.08/src' cp imagespread eledef eleredef edgeredef famdef ../bin/ make[1]: Leaving directory '/build/reproducible-path/repeatmasker-recon-1.08/src' @@ -557,8 +593,8 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'repeatmasker-recon' in '../repeatmasker-recon_1.08-8_amd64.deb'. dpkg-deb: building package 'repeatmasker-recon-dbgsym' in '../repeatmasker-recon-dbgsym_1.08-8_amd64.deb'. +dpkg-deb: building package 'repeatmasker-recon' in '../repeatmasker-recon_1.08-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../repeatmasker-recon_1.08-8_amd64.buildinfo dpkg-genchanges --build=binary -O../repeatmasker-recon_1.08-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -566,12 +602,14 @@ 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/1584778/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1584778/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/3731827 and its subdirectories -I: Current time: Wed Oct 21 13:50:16 -12 2026 -I: pbuilder-time-stamp: 1792633816 +I: removing directory /srv/workspace/pbuilder/1584778 and its subdirectories +I: Current time: Fri Sep 19 09:28:48 +14 2025 +I: pbuilder-time-stamp: 1758223728 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/repeatmasker-recon_1.08-8.diff: 85.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/repeatmasker-recon_1.08-8.diff.gz b2/build.log: 85.0% -- replaced with stdout Compressing the 1st log... b1/build.log: 85.9% -- replaced with stdout Thu Sep 18 19:28:50 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_repeatmasker-recon_unstable_amd64_1758223730 + touch /var/log/reproducible-builds/diffoscope_stamp_repeatmasker-recon_unstable_amd64_1758223730 + RESULT=0 + systemd-run '--description=diffoscope on repeatmasker-recon/1.08-8 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_28-73040 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu --run-session -c jenkins-reproducible-unstable-diffoscope-254e518d-74fb-4c45-86c4-a861233d87ac -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/dbd-tmp-vvKwChp ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/repeatmasker-recon_1.08-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/repeatmasker-recon_1.08-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/repeatmasker-recon_1.08-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/b1/repeatmasker-recon_1.08-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/b2/repeatmasker-recon_1.08-8_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_28-73040.service; invocation ID: ce7e09239ac7478c9f08a5493bb8079a # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/repeatmasker-recon_1.08-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/repeatmasker-recon_1.08-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/repeatmasker-recon_1.08-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/b1/repeatmasker-recon_1.08-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.BNxc6URu/b2/repeatmasker-recon_1.08-8_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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 227ms CPU time consumed: 191ms Memory peak: 17.2M (swap: 0B) _ _ _ __ ___ _ __ ___ __ _| |_ _ __ ___ __ _ ___| | _____ _ __ _ __ ___ | '__/ _ \ '_ \ / _ \/ _` | __| '_ ` _ \ / _` / __| |/ / _ \ '__|____| '__/ _ \ | | | __/ |_) | __/ (_| | |_| | | | | | (_| \__ \ < __/ | |_____| | | __/ |_| \___| .__/ \___|\__,_|\__|_| |_| |_|\__,_|___/_|\_\___|_| |_| \___| |_| ___ ___ _ __ / __/ _ \| '_ \ | (_| (_) | | | | \___\___/|_| |_| Thu Sep 18 19:28:50 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Thu Sep 18 19:28:50 UTC 2025 I: repeatmasker-recon from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-18 19:28:51] INFO: Starting at 2025-09-18 19:28:51.234856 [2025-09-18 19:28:51] INFO: Generating the pages of 1 package(s) [2025-09-18 19:28:51] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/repeatmasker-recon didn't produce a buildlog, even though it has been built. [2025-09-18 19:28:51] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/repeatmasker-recon didn't produce a buildlog, even though it has been built. [2025-09-18 19:28:51] INFO: Finished at 2025-09-18 19:28:51.552168, took: 0:00:00.317318 Thu Sep 18 19:28:51 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/repeatmasker-recon.html Thu Sep 18 19:28:51 UTC 2025 I: Removing signed repeatmasker-recon_1.08-8_amd64.buildinfo.asc files: removed './b1/repeatmasker-recon_1.08-8_amd64.buildinfo.asc' removed './b2/repeatmasker-recon_1.08-8_amd64.buildinfo.asc' 1758223731 amd64 unstable repeatmasker-recon Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/repeatmasker-recon_1.08-8.rbuild.log: 82.0% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/repeatmasker-recon_1.08-8.rbuild.log.gz [2025-09-18 19:28:51] INFO: Starting at 2025-09-18 19:28:51.943214 [2025-09-18 19:28:52] INFO: Generating the pages of 1 package(s) [2025-09-18 19:28:52] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/repeatmasker-recon didn't produce a buildlog, even though it has been built. [2025-09-18 19:28:52] INFO: Finished at 2025-09-18 19:28:52.307705, took: 0:00:00.364496 All cleanup done. Thu Sep 18 19:28:52 UTC 2025 - total duration: 0h 5m 3s. Thu Sep 18 19:28:52 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-yUrAovFI, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 5min 5.438s CPU time consumed: 3.513s Memory peak: 38.9M (swap: 0B)