Mon Jan 20 10:58:37 UTC 2025 I: starting to build gff2aplot/trixie/armhf on jenkins on '2025-01-20 10:58' Mon Jan 20 10:58:37 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_20/7141/console.log Mon Jan 20 10:58:37 UTC 2025 I: Downloading source for trixie/gff2aplot=2.0-15 --2025-01-20 10:58:37-- http://deb.debian.org/debian/pool/main/g/gff2aplot/gff2aplot_2.0-15.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2044 (2.0K) [text/prs.lines.tag] Saving to: ‘gff2aplot_2.0-15.dsc’ 0K . 100% 268M=0s 2025-01-20 10:58:37 (268 MB/s) - ‘gff2aplot_2.0-15.dsc’ saved [2044/2044] Mon Jan 20 10:58:37 UTC 2025 I: gff2aplot_2.0-15.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gff2aplot Binary: gff2aplot Architecture: any Version: 2.0-15 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://genome.crg.es/software/gfftools/GFF2APLOT.html Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/gff2aplot Vcs-Git: https://salsa.debian.org/med-team/gff2aplot.git Testsuite: autopkgtest Testsuite-Triggers: ghostscript, graphicsmagick, imagemagick Build-Depends: debhelper-compat (= 13) Package-List: gff2aplot deb science optional arch=any Checksums-Sha1: 469f99901a437f8b539b8b29be9cb0f392d6633b 328439 gff2aplot_2.0.orig.tar.gz 7f336c40811459aceb3ad0fbb2a81048732612a3 20764 gff2aplot_2.0-15.debian.tar.xz Checksums-Sha256: 33798a1f2877fc9d64aaf143c2e5bb909021b1f147c6718e61fbcc96cc65ccc3 328439 gff2aplot_2.0.orig.tar.gz 341ed9d8a0f8cf26c7c28cfad34cdc49e59230d16d8dc6afd3b9ecfd2ad5cbe7 20764 gff2aplot_2.0-15.debian.tar.xz Files: 8b269e236bcbacb1c70e4a3424940dc6 328439 gff2aplot_2.0.orig.tar.gz 53d9a4f53d588d060b186aa6226a687f 20764 gff2aplot_2.0-15.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmXAyPkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFfeQ/9FZfoiO4smc+53Q0Ezfb3fword/HVh/IR ggXK4Ki8h4AF0PHpAbWgSSD6mn1V3MnPw5yR2etGPeSSmHouK16GTNih1VK1J6Fm k3YtNWiJo5u87yJTpl9MLblhwf1OpBxty4FBVVHIKmOZe39dyKnvP/kidzvLP6OL P68MUqlHUVVqVaZVn/IuSZvAJgYW+XMrIGbgC/AkOHw0My8oZUcizBsUODiVPqQ3 C07LxsWzgxY4IGRzUEBQ+YYWogxxgyG4yXaXrCw9klDKoHKcCdtp2scA4fLKMsgb CbxhCHjt0B/7k+gVIceZYWejymIYF4ANLcTcFyrtQYjTmpfc8LptUIMxvoUC1WXD CX8yO+KyhRWPjj82m10IPXSDc6ZWTa/tszqEdMzaeT6Zuf4UTF/LMaCLhqZDS6cb vQwH+6RBF9Y3zXz4VJx8ux3B22QsgOYUTQi8yl6hWnM4SPiJj0WqW4e3lVp3W7yf bocCC2UBjg63fgJGpjXSt2AjzNf62IZG9flWRtw8l830GSOWt15Eb+q3WhK7dPmO q6LxzyJOhoCfx9SRTQSPq7rqRmJlXstVs/F0V/6bC9kYzf1jlN+ITUCmuf7m5zzL ELprqaA6vyeD2Zgvd7/kj7tNpZ09n9mSKT29OuH5ZCdRR8X/4s1ccCg70SMtO9Cr WLGbwv3ljTw= =Z4Vx -----END PGP SIGNATURE----- Mon Jan 20 10:58:37 UTC 2025 I: Checking whether the package is not for us Mon Jan 20 10:58:37 UTC 2025 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Mon Jan 20 10:58:37 UTC 2025 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Mon Jan 20 10:59:50 UTC 2025 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 19 22:58:43 -12 2025 I: pbuilder-time-stamp: 1737370723 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gff2aplot_2.0-15.dsc] I: copying [./gff2aplot_2.0.orig.tar.gz] I: copying [./gff2aplot_2.0-15.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gff2aplot_2.0-15.dsc: unsupported subcommand dpkg-source: info: extracting gff2aplot in gff2aplot-2.0 dpkg-source: info: unpacking gff2aplot_2.0.orig.tar.gz dpkg-source: info: unpacking gff2aplot_2.0-15.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying non_lexical_loop_iterator.patch dpkg-source: info: applying 02-blat2gff.diff dpkg-source: info: applying 03-parseblast.diff dpkg-source: info: applying use-dpkg-buildflags.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying fis-privacy-breach.patch dpkg-source: info: applying perl_5.28.patch dpkg-source: info: applying fix_install_ali2gff.patch dpkg-source: info: applying enhance_sprintf_buffer.patch dpkg-source: info: applying fix_README_used_for_test.patch dpkg-source: info: applying fix_gff_comments.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/23243/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='92ca56f460c6417d8b893e2dfb0de046' 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='23243' 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.tN7XN3ds/pbuilderrc_0ujA --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.tN7XN3ds/b1 --logfile b1/build.log gff2aplot_2.0-15.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64c 6.1.0-30-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/23243/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: armhf 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 ... 19569 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.6 MB of archives. After unpacking 74.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-4 [196 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.4-1 [84.6 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-4 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.23 [90.6 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.5.4-2 [539 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-6 [9086 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-4 [1489 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.23 [919 kB] Fetched 19.6 MB in 1s (37.0 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 ... 19569 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-4_armhf.deb ... Unpacking gettext-base (0.22.5-4) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_armhf.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-1_armhf.deb ... Unpacking bsdextrautils (2.40.4-1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_armhf.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-4_all.deb ... Unpacking autopoint (0.22.5-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.23_all.deb ... Unpacking libdebhelper-perl (13.23) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../21-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libunistring5:armhf. Preparing to unpack .../23-libunistring5_1.3-1_armhf.deb ... Unpacking libunistring5:armhf (1.3-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-6_armhf.deb ... Unpacking libicu72:armhf (72.1-6) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.22.5-4_armhf.deb ... Unpacking gettext (0.22.5-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.23_all.deb ... Unpacking debhelper (13.23) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libicu72:armhf (72.1-6) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.23) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-4) ... Setting up m4 (1.4.19-5) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunistring5:armhf (1.3-1) ... Setting up autopoint (0.22.5-4) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-4) ... Setting up libtool (2.5.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.23) ... Processing triggers for libc-bin (2.40-5) ... 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/gff2aplot-2.0/ && 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 > ../gff2aplot_2.0-15_source.changes dpkg-buildpackage: info: source package gff2aplot dpkg-buildpackage: info: source version 2.0-15 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/gff2aplot-2.0' rm -f src/ali2gff/ali2gff bin/* make[1]: Leaving directory '/build/reproducible-path/gff2aplot-2.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/gff2aplot-2.0' ### ### RUNNING MAKEFILE ### ### Mon Jan 20 10:59:28 2025 -- pbuilder1 ### Finishing PERL script from "src/gff2aplot.pl" -> "bin/gff2aplot.pl" ### ### Finishing PERL script from "src/parseblast.pl" -> "bin/parseblast.pl" ### Finishing PERL script from "src/blat2gff.pl" -> "bin/blat2gff.pl" ### Finishing PERL script from "src/sim2gff.pl" -> "bin/sim2gff.pl" ### Making ALI2GFF... make[2]: Entering directory '/build/reproducible-path/gff2aplot-2.0/src/ali2gff' ### ### MAKEFILE DONE... ### ali2gff.c: In function 'main': ali2gff.c:88:15: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] 88 | char *ptr; | ^~~ ali2gff.c: In function 'processGFFfile': ali2gff.c:355:113: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 355 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\n", xName,yName,source,xb,yb,xe,ye,scores,strands,frames); | ^~ ~~~~~ In file included from /usr/include/stdio.h:970, from ali2gff.h:20, from ali2gff.c:64: In function 'sprintf', inlined from 'processGFFfile' at ali2gff.c:355:44: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 4028) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function 'processGFFfile': ali2gff.c:354:113: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 354 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\n",xName,yName,source,xb,yb,xe,ye,score ,strands,frames); | ^~ ~~~~~ In function 'sprintf', inlined from 'processGFFfile' at ali2gff.c:354:44: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 2034) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function 'processGFFfile': ali2gff.c:351:113: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 351 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\t%s", xName,yName,source,xb,yb,xe,ye,scores,strands,frames,cptr); | ^~ ~~~~~ In function 'sprintf', inlined from 'processGFFfile' at ali2gff.c:351:44: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 4028) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function 'processGFFfile': ali2gff.c:350:113: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 350 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\t%s",xName,yName,source,xb,yb,xe,ye,score ,strands,frames,cptr); | ^~ ~~~~~ In function 'sprintf', inlined from 'processGFFfile' at ali2gff.c:350:44: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 2034) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function 'processGFFfile': ali2gff.c:300:113: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 300 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\n", yName,xName,source,yb,xb,ye,xe,scores,strands,frames); | ^~ ~~~~~ In function 'sprintf', inlined from 'processGFFfile' at ali2gff.c:300:44: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 4028) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function 'processGFFfile': ali2gff.c:299:113: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 299 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\n",yName,xName,source,yb,xb,ye,xe,score,strands,frames); | ^~ ~~~~~ In function 'sprintf', inlined from 'processGFFfile' at ali2gff.c:299:44: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 2034) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function 'processGFFfile': ali2gff.c:296:113: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 296 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\t%s", yName,xName,source,yb,xb,ye,xe,scores,strands,frames,cptr); | ^~ ~~~~~ In function 'sprintf', inlined from 'processGFFfile' at ali2gff.c:296:44: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 4028) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function 'processGFFfile': ali2gff.c:295:113: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 295 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\t%s",yName,xName,source,yb,xb,ye,xe,score,strands,frames,cptr); | ^~ ~~~~~ In function 'sprintf', inlined from 'processGFFfile' at ali2gff.c:295:44: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 2034) into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ali2gff.c: In function 'processMumfile': ali2gff.c:732:40: warning: 'score' may be used uninitialized [-Wmaybe-uninitialized] 732 | score = (score - errCount)/score; // match percentage | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:420:15: note: 'score' was declared here 420 | float score; | ^~~~~ ali2gff.c:840:67: warning: 'fxb' may be used uninitialized [-Wmaybe-uninitialized] 840 | fxe = fxb + flen - 1; | ~~~~^~~~~~ ali2gff.c:421:27: note: 'fxb' was declared here 421 | unsigned long int fxb, fxe, fyb, fye; // start and end positions of gaps resp. fragments of gaps | ^~~ ali2gff.c:841:67: warning: 'fyb' may be used uninitialized [-Wmaybe-uninitialized] 841 | fye = fyb + flen - 1; | ~~~~^~~~~~ ali2gff.c:421:37: note: 'fyb' was declared here 421 | unsigned long int fxb, fxe, fyb, fye; // start and end positions of gaps resp. fragments of gaps | ^~~ ali2gff.c: In function 'processSimfile': ali2gff.c:1064:36: warning: 'xseqLen_4' may be used uninitialized [-Wmaybe-uninitialized] 1064 | if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:997:27: note: 'xseqLen_4' was declared here 997 | unsigned long int xseqLen_4; /* length of x sequence -5 */ | ^~~~~~~~~ ali2gff.c:1064:62: warning: 'yseqLen_4' may be used uninitialized [-Wmaybe-uninitialized] 1064 | if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:998:27: note: 'yseqLen_4' was declared here 998 | unsigned long int yseqLen_4; /* length of y sequence -5 */ | ^~~~~~~~~ ali2gff.c: In function 'main': ali2gff.c:135:9: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation] 135 | strncpy(infile,argv[1],MAXSTRING); | ^ make[2]: Leaving directory '/build/reproducible-path/gff2aplot-2.0/src/ali2gff' mkdir -p ./bin cp ./src/ali2gff/ali2gff \ ./bin/ali2gff mode of 'bin/gff2aplot.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/parseblast.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/blat2gff.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/sim2gff.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) make[1]: Leaving directory '/build/reproducible-path/gff2aplot-2.0' dh_auto_test make -j3 test make[1]: Entering directory '/build/reproducible-path/gff2aplot-2.0' ### SORRY !!! Tests were not implemented yet... make[1]: Leaving directory '/build/reproducible-path/gff2aplot-2.0' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/gff2aplot-2.0' for script in `find bin -name "*.pl"` ; do mv $script bin/`basename $script .pl` ; done make[1]: Leaving directory '/build/reproducible-path/gff2aplot-2.0' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/gff2aplot-2.0' dh_installexamples # Fix path names, silence GS find debian/*/usr/share/doc/*/examples -name README -exec sed -i \ -e 's?^$BIN/\([0-9a-z]\+\)\.pl?\1?' \ -e 's?^$BIN/\([0-9a-z]\+\) ?\1 ?' \ -e 's?^GS=.*;?GS="gs -q" ;?' \{\} \; make[1]: Leaving directory '/build/reproducible-path/gff2aplot-2.0' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gff2aplot' in '../gff2aplot_2.0-15_armhf.deb'. dpkg-deb: building package 'gff2aplot-dbgsym' in '../gff2aplot-dbgsym_2.0-15_armhf.deb'. dpkg-genbuildinfo --build=binary -O../gff2aplot_2.0-15_armhf.buildinfo dpkg-genchanges --build=binary -O../gff2aplot_2.0-15_armhf.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/23243 and its subdirectories I: Current time: Sun Jan 19 22:59:44 -12 2025 I: pbuilder-time-stamp: 1737370784 Mon Jan 20 10:59:53 UTC 2025 I: 1st build successful. Starting 2nd build on remote node wbq0-armhf-rb.debian.net. Mon Jan 20 10:59:53 UTC 2025 I: Preparing to do remote build '2' on wbq0-armhf-rb.debian.net. Mon Jan 20 11:03:17 UTC 2025 I: Deleting $TMPDIR on wbq0-armhf-rb.debian.net. Mon Jan 20 11:03:20 UTC 2025 I: gff2aplot_2.0-15_armhf.changes: Format: 1.8 Date: Mon, 05 Feb 2024 12:09:38 +0100 Source: gff2aplot Binary: gff2aplot gff2aplot-dbgsym Architecture: armhf Version: 2.0-15 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gff2aplot - pair-wise alignment-plots for genomic sequences in PostScript Closes: 1044834 Changes: gff2aplot (2.0-15) unstable; urgency=medium . * Fix clean target Closes: #1044834 * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: efef7762632b33bb3f17da55924f4697fef1f7cf 25624 gff2aplot-dbgsym_2.0-15_armhf.deb 319fcd59837c73933cd739ed25bc67d680a73cbf 4834 gff2aplot_2.0-15_armhf.buildinfo ab72aefc1cb8a10221289c14dd4ec29ff9986010 244052 gff2aplot_2.0-15_armhf.deb Checksums-Sha256: 96ccd5b1a5d31c59525d375d1530bcaf4f797270bcc74df277fb7c480a9aaadc 25624 gff2aplot-dbgsym_2.0-15_armhf.deb 169b88bf2bc5c2e4926e0fe1db963bfde6d585e1ae484d03a69f7539b0f430ea 4834 gff2aplot_2.0-15_armhf.buildinfo 1ac1e5cf8475d52af3acab84093aaebec8732663dd2006597ac2ae44f46104d2 244052 gff2aplot_2.0-15_armhf.deb Files: 53070a73f42ef47bc61b4668330a46c4 25624 debug optional gff2aplot-dbgsym_2.0-15_armhf.deb 1a9755a888175f856dd0300841d7c1ca 4834 science optional gff2aplot_2.0-15_armhf.buildinfo a1eecdb51f7d89a47189a3c7d72a6984 244052 science optional gff2aplot_2.0-15_armhf.deb Mon Jan 20 11:03:21 UTC 2025 I: diffoscope 285 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_20-7141.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.tN7XN3ds/gff2aplot_2.0-15.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.tN7XN3ds/gff2aplot_2.0-15.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.tN7XN3ds/gff2aplot_2.0-15.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.tN7XN3ds/b1/gff2aplot_2.0-15_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.tN7XN3ds/b2/gff2aplot_2.0-15_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.425s) 0.425s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.021s) 0.021s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 795ms CPU time consumed: 796ms Mon Jan 20 11:03:22 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists. Mon Jan 20 11:03:22 UTC 2025 I: gff2aplot from trixie built successfully and reproducibly on armhf. Mon Jan 20 11:03:24 UTC 2025 I: Submitting .buildinfo files to external archives: Mon Jan 20 11:03:24 UTC 2025 I: Submitting 8.0K b1/gff2aplot_2.0-15_armhf.buildinfo.asc Mon Jan 20 11:03:25 UTC 2025 I: Submitting 8.0K b2/gff2aplot_2.0-15_armhf.buildinfo.asc Mon Jan 20 11:03:25 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jan 20 11:03:25 UTC 2025 I: Done submitting .buildinfo files. Mon Jan 20 11:03:25 UTC 2025 I: Removing signed gff2aplot_2.0-15_armhf.buildinfo.asc files: removed './b1/gff2aplot_2.0-15_armhf.buildinfo.asc' removed './b2/gff2aplot_2.0-15_armhf.buildinfo.asc'